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Topic: Stochastic tunneling

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	Stochastic Optimization Methods
		Stochastic optimization methods are now being used in a multitude of applications, ranging from circuit design on silicon wafers to airline flight schedules.
		Stochastic optimization methods successively improve one or several configurations of the underlying model to obtain an approximant of the global optimum of the PES.
		An alternate approach to simplify the underlying PES is used in the stochastic tunneling method, where the dynamical process explores the transformed potential energy surface.
	iwrwww1.fzk.de /biostruct/Opti/opti.htm (945 words)

	[No title]
		Stochastic (non-deterministic) ideas may also be incorporated in gradient search-based optimization, thus leading to stochastic gradient algorithms.
		The stochastic gradient algorithm in Equation (8.1.4) is inspired by the dynamics of the diffusion process in physical phenomena such as atomic migration in crystals or chemical reactions.
		Also, stochastic gradient search has a better chance of escaping local minima and areas of shallow gradient, which may allow it to converge faster (Hoptroff and Hall, 1989).
	neuron.eng.wayne.edu /tarek/MITbook/chap8/8_1.html (2081 words)

	Adaptation in stochastic tunneling global optimization of complex potential energy landscapes
		One particular successful approach is the usage of tunneling functions to cross barriers and transition states more easily thus allowing for a fast scan of the potential energy surface under investigation.
		In this paper we develop for the first time a performance measurement procedure for stochastic tunneling approaches and derive an adaptive algorithm that is steered by this performance measure.
		The proposed algorithm is based on a scale-free measure and thus applicable to general stochastic optimization schemes.
	www.edpsciences.org /articles/epl/abs/2006/12/epl9396/epl9396.html (188 words)

	Application of the Stochastic Tunneling Method for Computational High Trhoughpur Screening
		An initial investigation revealed that a novel optimization method, the stochastic tunneling method (STUN) [1] was superior in performance and accuracy for rigid ligand docking in comparison to a number of other widely used stochastic optimization techniques (see Fig 1)[2].
		This approach to docking is thus able to identify the important characteristics of the receptor even in the absence of the crystal structure with the ligand and able to suggest experimental tests of this hypothesis.">
		The two most important ingredients in this approach are the choice of the scoring function and the reliability and efficiency of the optimization method that is used to find the optimal orientation for each of the ligands.
	www.nsti.org /Nanotech2003/showabstract.html?absno=256 (599 words)

	Power-constrained CMOS scaling limits
		Oxide tunneling between gate and channel is the most prominent and well known of these leakage currents, and is illustrated in Figure 3.
		In n-FETs this current is due to the tunneling of electrons from the channel to the gate.
		In p-FETs the tunneling current may be due to hole tunneling from channel to gate for very thin oxides (<1.5 nm) and low voltages, but at higher bias it is more often due to tunneling of electrons from the valence band of the gate into the conduction band of the body.
	www.research.ibm.com /journal/rd/462/frank.html (4605 words)

	ScienceWeek
		Among these systems, a magnetic tunnel junction, which consists of two ferromagnetic metal layers (electrodes) separated by a thin insulating layer (tunnel barrier) and shows the tunnel magnetoresistance effect (3-5), is especially important for application to magnetoresistive random-access memory devices.
		For example, the resonant-tunneling effect (i.e., coherent tunneling of electrons from one electrode to the other through quantum well states formed between the two electrodes), in which the coherence of electron wave functions is essential, has never been well controlled in spin-polarized systems such as magnetic tunnel junctions and magnetic semiconductors.
		Spin-polarized resonant tunneling is crucial for the development of highly functional devices, such as a resonant-tunneling spin transistor and quantum information devices, because the coherency of both the wave functions and the spins of conduction electrons should be conserved in those devices.
	scienceweek.com /2002/sw020823.htm (10788 words)

	Stochastic Tunnels in Evolutionary Dynamics -- Iwasa et al. 166 (3): 1571 -- Genetics
		We refer to the latter transition as "stochastic tunneling."
		The solid line uses the tunneling rate as given by Equation 6 and Equation 8.
		Alternatively, a type 2 cell can be produced before the type 1 cell has taken over the compartment, such that the compartment moves from state 0 directly to state 2 without ever visiting state 1.
	www.genetics.org /cgi/content/full/166/3/1571 (4517 words)

	Additions to the Stochastic Programming Bibliography
		Stochastic approximation for nonexpansive maps: application to Q-learning algorithms.
		Stochastic optimization for operating chemical processes under uncertainty.
		A class of stochastic optimization problems with one quadratic and several linear objective functions and extended portfolio selection model.
	mally.eco.rug.nl /biblio/update.htm (4090 words)

	Stochastic Resonance and Receptor Function
		The original paper that describe the stochastic resonance phenomenon in crayfish vibration detectors assumed that the noise came from the crayfish's external environment.
		Should you wish to investigate the stochastic resonance phenomenon further, here are a few references that will help you get access to the rapidly accumulating literature on the subject.
		Stochastic resonance and the benefits of noise: From ice ages to crayfish and squids.
	www.unm.edu /~toolson/435stochrese.html (1501 words)

	[No title]
		Reinhard Werner: A generalization of stochastic mechanics and its relation to quantum mechanics, Phys.Rev.D 34,2 (1986) 463-469 J.A. Wheeler and W.H. Zurek (eds.): Quantum Theory and Measurement, Princeton Univ Press, 1983 E.P. Wigner: On the quantum correction for thermodynamic equilibrium, Phys.Rev. 40 (June 1932) 749-759 Introduces "Wigner transform".
		The stochastic quantization procedure is explained in much detail and it is found to possess remarkable features which can not be achieved within the conventional framework of quantum theory.
		Yasue: Stochastic quantization of wave fields and its application to dissipatively interacting fields, Journal of Mathematical Physics 19,9 (Sept. 1978) 1892-1897 K.
	www.math.temple.edu /~wds/homepage/pu-qm-bib (5757 words)

	Stochastic Tunnels in Evolutionary Dynamics -- Iwasa et al. 166 (3): 1571 -- Genetics
		Stochastic Tunnels in Evolutionary Dynamics -- Iwasa et al.
		"stochastic tunnel" arises, when the population moves from all
		rate of stochastic tunneling for the case when type 1 is as
	www.genetics.org /cgi/content/abstract/166/3/1571 (295 words)

	IngentaConnect A Multi-Nano-Dot Circuit and Structure Using Thermal-Noise-Assist... (Site not responding. Last check: 2007-10-20)
		In stochastic associative processing, the association probability of each stored pattern depends on the similarity between the stored pattern and the input pattern.
		Such unique processing is useful for sequential stochastic association and for clustering for vector quantization.
		We analyze the operation of this circuit in detail and propose for it a stochastic associative processing operation, where the detection timing of the electron position controls the association probability distribution.
	www.ingentaconnect.com /content/asp/jnn/2002/00000002/F0020003/art00011 (254 words)

	Stochastic Optimization Methods
		The freezing problem in stochastic minimization methods arises when the energy difference between ``adjacent'' local minima on the PES is much smaller than the energy of intervening transition states separating them.
		Adjusting the temperature to maintain a particular average effective energy balances the tunneling and the local-search phases of the algorithm.
		For the success of the method it is essential that the minimization process spends some time tunneling and some time searching at any stage of the minimization process.
	iwrwww1.fzk.de /biostruct/Opti/stun.htm (556 words)

	Bohmian mechanics "dsproved"
		This is a theorem,\nandgt; so attempts to find a case where Bohmian mechanics gives a\nandgt; different prediction to regular qm are like attempts to trisect\nandgt; an angle with a straight edge and compass.
		The quantities to which he is referring,\nnamely the dwell, transmission and reflection times, which correspond\nto the intuitive notions of the amount of time the various particles\nspend in a particular region, are not measurable in the context\nthat he describes.
		And\nandgt;also between Nelsons Stochastic, where the mean tunneling time is also a\nandgt;meaningful concept.\n\nThe question is not whether the concept is meaningful, but whether it\ncorresponds to anything in the actual world, and, if so, which\ntheory correctly predicts it.
	www.physicsforums.com /showthread.php?t=58815 (7627 words)

	Stochastic tunneling - Wikipedia, the free encyclopedia
		Stochastic tunneling (STUN) is one approach to global optimization among several others and is based on the Monte Carlo method-sampling of the function to be minimized.
		Schematic one-dimensional test function (fl) and STUN effective potential (red and blue), where the minimum indicated by the arrows is the best minimum found so far.
		The general idea of STUN is to circumvent the slow dynamics of ill-shaped energy functions that one encounters for example in spin glasses by tunneling through such barriers.
	en.wikipedia.org /wiki/Stochastic_tunneling (257 words)

	Simulated annealing - Wikipedia, the free encyclopedia
		Stochastic tunneling is a particular successful attempt to overcome the increasing difficulty simulated annealing runs have in escaping from local minima as the temperature decreases.
		Stochastic tunneling pushes the optimization run out of local minima, 'tunneling' through barriers.
		Tabu search (TS) is similar to simulated annealing, in that both traverse the solution space by testing neighbours of the current solution.
	en.wikipedia.org /wiki/Simulated_annealing (3112 words)

	No Title
		N. Alberding, H. Frauenfelder, and P. Hänggi, Stochastic Theory of Ligand Migration in Biomolecules: CO-Myoglobin Binding, Proc.
		P. Hänggi, Stochastic Theory for the Kinetics of Migration of Ligands in Biomolecules,
		S.J. Linz, M. Raible and P. Hänggi, Stochastic field equation for amorphous surface growth, Lecture Notes in Physics: "Stochastic Processes in Physics", J. Freund and T. Pöschl, eds., Springer Verlag (Berlin, Heidelberg 2000), Vol.
	www.physik.uni-augsburg.de /theo1/hanggi/PubH.html (5742 words)

	Dr. Jose L. Mateos homepage
		In particular, I am interested in the problem of tunneling times, that is, the determination of the time that a particle spent during the process of tunneling through a potential barrier.
		Another line of research that I am starting is related with the problem of transport in Stochastic or Thermal Ratchets and Stochastic Resonance.
		The phenomenon of stochastic resonance has to do with the enhancement of the signal-to-noise ratio by adding noise, and has been found recently in many physical and biological systems.
	scifunam.fisica.unam.mx /jlm/mateos.html (610 words)

	echeminfo -colayer web conversations dynamic version (Site not responding. Last check: 2007-10-20)
		In addition we were able to reproducibly fold several helical proteins, ranging 20-60 amino acids in size from random starting conditions.
		We used several stochastic optimization methods: the stochastic tunneling method, an adapted version of parallel tempering, basin hopping techniques and distributed evolutionary optimization strategies.
		We will discuss advantages and limitations with respect to further improvements of this approach to in-silico all-atom protein structure prediction.
	echeminfo.colayer.net /COMTY_mewenzel (271 words)

	OR Graduate Courses
		Also included are stochastic inventory systems of lot sized-reorder type; periodic review and single-period models; application of dynamic programming theory to deterministic and stochastic cases; and static and dynamic production-planning models.
		An advanced topic chosen according to interests of students and the instructor from dynamic programming, inventory theory, queuing theory, Markov and semi-Markov decision processes, reliability theory, decision theory, network flows, large-scale linear programming, nonlinear programming, and combinatorics.
		Contents vary and may include topics in optimization, stochastic methods, or decision support that are not covered in the standard OR curriculum.
	www.gmu.edu /departments/seor/courses/or-grad-courses.html (1663 words)

	The role of chromosomal instability in tumor initiation -- Nowak et al. 99 (25): 16226 -- Proceedings of the National ...
		Tunnels occur if the second step in a consecutive transition is much faster than the first one and if the final cell has a strong selective advantage.
		Transition rates and stochastic tunnels of the probabilistic process describing the dynamics of early steps in colon cancer.
		The exact conditions for tunneling are as follows.
	www.pnas.org /cgi/content/full/99/25/16226 (4371 words)

	Operations Research (OR) - University Catalog 2006-07: George Mason University
		Covers linear programming model and simplex method of solution, duality, and sensitivity analysis; transportation and assignment problems; shortest path and maximal flow problems; and introduction to integer and nonlinear programming.
		Covers convex sets and functions, optimality criteria and duality; algorithms for unconstrained minimization, including descent methods, conjugate directions, Newton-type and quasi-Newton methods; and algorithms for constrained optimization, including active set methods and penalty and barrier methods.
		Contents vary; possible topics include statistical analysis of simulation output data, random number and random ariate generation, variance reduction techniques, sensitivity analysis and optimization of simulation models, distributed and parallel simulation, object-oriented simulation, and specialized applications.
	www.gmu.edu /catalog/courses/or.html (2194 words)

	An All-Atom Force Field for Tertiary Structure Prediction of Helical Proteins -- Herges and Wenzel 87 (5): 3100 -- ...
		the protein was predicted correctly in 8 of 25 stochastic tunneling
		Reproducible protein folding with the stochastic tunneling method.
		Stochastic tunneling approach for global optimization of complex potential energy landscapes.
	www.biophysj.org /cgi/content/full/87/5/3100 (4175 words)

	Prof. Linda E. Reichl @ Center for Complex Quantum Systems
		Her research has ranged over a number of topics in statistical physics and nonlinear dynamics.
		They include the theory of low temperature Fermi liquids, quantum transport theory, application of linear hydrodynamics to translational and rotational Brownian motion and dielectric response, the transition to chaos in classical and quantum mechanical conservative systems and the new field of 'stochastic chaos' theory.
		She has published more than 100 research papers, has written three books, and has edited several books.
	order.ph.utexas.edu /people/Reichl.htm (813 words)

	A Bond-Fluctuation Mechanism for Stochastic Switching in Wired Molecules -- Ramachandran et al. 300 (5624): 1413 -- ...
		A Bond-Fluctuation Mechanism for Stochastic Switching in Wired Molecules -- Ramachandran et al.
		Realization of a four-step molecular switch in scanning tunneling microscope manipulation of single chlorophyll-a molecules.
		Molecular Electronics Special Feature: Probing charge transport at the single-molecule level on silicon by using cryogenic ultra-high vacuum scanning tunneling microscopy.
	www.sciencemag.org /cgi/content/short/300/5624/1413 (390 words)

	Bookkeepingmechanics: Accounting viewed as bouncing particles
		Strong wealth condensation in stochastic transfer potential economies
		We analyze wealth condensation for a wide class of stochastic economy models on the basis of the economic analog
		Wealth condensation is the result of stochastic tunneling through a metastable
	www.bookkeepingmechanics.com (582 words)

	Enhanced Stem Cell Survival in Familial Adenomatous Polyposis -- Kim et al. 164 (4): 1369 -- American Journal of ...
		other mutations before fixation) is similar to the stochastic
		tunneling progression shortcut described by Nowak and colleagues.
		APC mutations appear to be common in cancers because they confer
	ajp.amjpathol.org /cgi/content/full/164/4/1369 (5064 words)

	[No title]
		One example of this, presented here, is the use of the grand canonical ensemble of statistical physics to elaborate game theory in which the number of players is not pre-determined, but varies stochastically.
		Another example is how to apply steepest descent techniques to optimize/control systems of discrete variables.
		I will discuss three approaches based on (1) systems of ODE with nonlinearity, (1) stochastic processes with irreversibility, and (3) constraint-based optimization suggesting an oriented matroid.
	www.math.uci.edu /~komarova/seminar.html (5672 words)

	NIST Technicalendar Online
		We have implemented a fast and sensitive electrometer, based on the measurement of the complex (Josephson) impedance of a Cooper-pair transistor.
		With this measurement technique the charge read-out is accomplished enitrely on the supercurrent branch, allowing us to look in real-time on quasiparticle tunneling in the transistor.
		I will address these questions, and will further present data from our measurements of quasiparticle tunneling rates in single and multi- transistor circuits.
	nvl.nist.gov /pub/nistpubs/calendars/techcal/2006/061203-tc.htm (1362 words)

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