Biomedical subjects

M A Novotny

Publications and source records attributed to M A Novotny.

16 recordsLinked to original sources

PubMed2006

Efficiency of rejection-free dynamic Monte Carlo methods for homogeneous spin models, hard disk systems, and hard sphere systems.

We construct asymptotic arguments for the relative efficiency of rejection-free Monte Carlo (MC) methods compared to the standard MC method. We find that the efficiency is proportional to exp(constbeta) in the Ising, sqrt[beta] in the classical XY, and beta in the classical Heisenberg spin systems with inverse temperature beta, regardless of the dimension. The efficiency in hard particle systems is also obtained, and found to be proportional to (rho(cp)-rho)(-d) with the closest packing density rho(cp), density rho, and dimension d of the systems. We construct and implement a rejection-free Monte Carlo method for the hard-disk system. The RFMC has a greater computational efficiency at high densities, and the density dependence of the efficiency is as predicted by our arguments.

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PubMed2006

Synchronization landscapes in small-world-connected computer networks.

Motivated by a synchronization problem in distributed computing we studied a simple growth model on regular and small-world networks, embedded in one and two dimensions. We find that the synchronization landscape (corresponding to the progress of the individual processors) exhibits Kardar-Parisi-Zhang-like kinetic roughening on regular networks with short-range communication links. Although the processors, on average, progress at a nonzero rate, their spread (the width of the synchronization landscape) diverges with the number of nodes (desynchronized state) hindering efficient data management. When random communication links are added on top of the one and two-dimensional regular networks (resulting in a small-world network), large fluctuations in the synchronization landscape are suppressed and the width approaches a finite value in the large system-size limit (synchronized state). In the resulting synchronization scheme, the processors make close-to-uniform progress with a nonzero rate without global intervention. We obtain our results by "simulating the simulations," based on the exact algorithmic rules, supported by coarse-grained arguments.

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PubMed2006

Universal scaling in mixing correlated growth with randomness.

We study two-component growth that mixes random deposition (RD) with a correlated growth process that occurs with probability p. We find that these composite systems are in the universality class of the correlated growth process. For RD blends with either Edwards-Wilkinson or Kardar-Parisi-Zhang processes, we identify a nonuniversal exponent in the universal scaling in p.

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PubMed2004

Roughening of the interfaces in (1+1) -dimensional two-component surface growth with an admixture of random deposition.

We simulate competitive two-component growth on a one-dimensional substrate of L sites. One component is a Poisson-type deposition that generates Kardar-Parisi-Zhang (KPZ) correlations. The other is random deposition (RD). We derive the universal scaling function of the interface width for this model and show that the RD admixture acts as a dilatation mechanism to the fundamental time and height scales, but leaves the KPZ correlations intact. This observation is generalized to other growth models. It is shown that the flat-substrate initial condition is responsible for the existence of an early nonscaling phase in the interface evolution. The length of this initial phase is a nonuniversal parameter, but its presence is universal. We introduce a method to measure the length of this initial nonscaling phase. In application to parallel and distributed computations, the important consequence of the derived scaling is the existence of the upper bound for the desynchronization in a conservative update algorithm for parallel discrete-event simulations. It is shown that such algorithms are generally scalable in a ring communication topology.

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PubMed2004

Low-temperature nucleation in a kinetic Ising model under different stochastic dynamics with local energy barriers.

Using both analytical and simulational methods, we study low-temperature nucleation rates in kinetic Ising lattice-gas models that evolve under two different Arrhenius dynamics that interpose between the Ising states a transition state representing a local energy barrier. The two dynamics are the transition-state approximation [T. Ala-Nissila, J. Kjoll, and S. C. Ying, Phys. Rev. B 46, 846 (1992)] and the one-step dynamic [H. C. Kang and W. H. Weinberg, J. Chem. Phys. 90, 2824 (1989)]. Even though they both obey detailed balance and are here applied to a situation that does not conserve the order parameter, we find significant differences between the nucleation rates observed with the two dynamics, and between them and the standard Glauber dynamic [R. J. Glauber, J. Math. Phys. 4, 294 (1963)], which does not contain transition states. Our results show that great care must be exercised when devising kinetic Monte Carlo transition rates for specific physical or chemical systems.

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PubMed2004

Evolution of time horizons in parallel and grid simulations.

We analyze the evolution of the local simulation times (LST) in parallel discrete event simulations. The new ingredients introduced are (i) we associate the LST with the nodes and not with the processing elements, and (ii) we propose to minimize the exchange of information between different processing elements by freezing the LST on the boundaries between processing elements for some time of processing and then releasing them by a wide-stream memory exchange between processing elements. The highlights of our approach are (i) it keeps the highest level of processor time utilization during the algorithm evolution, (ii) it takes a reasonable time for the memory exchange, excluding the time consuming and complicated process of message exchange between processors, and (iii) the communication between processors is decoupled from the calculations performed on a processor. The effectiveness of our algorithm grows with the number of nodes (or threads). This algorithm should be applicable for any parallel simulation with short-range interactions, including parallel or grid simulations of partial differential equations.

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PubMed2004

Low-temperature nucleation in a kinetic Ising model with soft stochastic dynamics.

We study low-temperature nucleation in kinetic Ising models by analytical and simulational methods, confirming the general result for the average metastable lifetime, =Aexp((betagamma) (beta=1/k(B)T) [Commun. Math. Phys. 137, 209 (1991)]]. Contrary to common belief, we find that both A and Gamma depend significantly on the stochastic dynamic. In particular, for a "soft" dynamic, in which the effects of the interactions and the applied field factorize in the transition rates, Gamma does not simply equal the energy barrier against nucleation, as it does for the standard Glauber dynamic, which does not have this factorization property.

Cold Temperature↗

PubMed2003

Update statistics in conservative parallel-discrete-event simulations of asynchronous systems.

We model the performance of an ideal closed chain of L processing elements that work in parallel in an asynchronous manner. Their state updates follow a generic conservative algorithm. The conservative update rule determines the growth of a virtual time surface. The physics of this growth is reflected in the utilization (the fraction of working processors) and in the interface width. We show that it is possible to make an explicit connection between the utilization and the microscopic structure of the virtual time interface. We exploit this connection to derive the theoretical probability distribution of updates in the system within an approximate model. It follows that the theoretical lower bound for the computational speedup is s=(L+1)/4 for L> or =4. Our approach uses simple statistics to count distinct surface-configuration classes consistent with the model growth rule. It enables one to compute analytically microscopic properties of an interface, which are unavailable by continuum methods.

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PubMed2003

Algorithmic scalability in globally constrained conservative parallel discrete event simulations of asynchronous systems.

We consider parallel simulations for asynchronous systems employing L processing elements that are arranged on a ring. Processors communicate only among the nearest neighbors and advance their local simulated time only if it is guaranteed that this does not violate causality. In simulations with no constraints, in the infinite L limit the utilization scales [Korniss et al., Phys. Rev. Lett. 84, 1351 (2000)]; but, the width of the virtual time horizon diverges (i.e., the measurement phase of the algorithm does not scale). In this work, we introduce a moving Delta-window global constraint, which modifies the algorithm so that the measurement phase scales as well. We present results of systematic studies in which the system size (i.e., L and the volume load per processor) as well as the constraint are varied. The Delta constraint eliminates the extreme fluctuations in the virtual time horizon, provides a bound on its width, and controls the average progress rate. The width of the Delta window can serve as a tuning parameter that, for a given volume load per processor, could be adjusted to optimize the utilization, so as to maximize the efficiency. This result may find numerous applications in modeling the evolution of general spatially extended short-range interacting systems with asynchronous dynamics, including dynamic Monte Carlo studies.

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PubMed2003

Rejection-free Monte Carlo algorithms for models with continuous degrees of freedom.

We construct a rejection-free Monte Carlo algorithm for a system with continuous degrees of freedom. We illustrate the algorithm by applying it to the classical three-dimensional Heisenberg model with canonical Metropolis dynamics. We obtain the lifetime of the metastable state following a reversal of the external magnetic field. Our rejection-free algorithm obtains results in agreement with a direct implementation of the Metropolis dynamic and requires orders of magnitude less computational time at low temperatures. The treatment is general and can be extended to other dynamics and other systems with continuous degrees of freedom.

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PubMed2003

Suppressing roughness of virtual times in parallel discrete-event simulations.

In a parallel discrete-event simulation (PDES) scheme, tasks are distributed among processing elements (PEs) whose progress is controlled by a synchronization scheme. For lattice systems with short-range interactions, the progress of the conservative PDES scheme is governed by the Kardar-Parisi-Zhang equation from the theory of nonequilibrium surface growth. Although the simulated (virtual) times of the PEs progress at a nonzero rate, their standard deviation (spread) diverges with the number of PEs, hindering efficient data collection. We show that weak random interactions among the PEs can make this spread nondivergent. The PEs then progress at a nonzero, near-uniform rate without requiring global synchronizations.

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PubMed2002

Absence of first-order transition and tricritical point in the dynamic phase diagram of a spatially extended bistable system in an oscillating field.

It has been well established that spatially extended, bistable systems that are driven by an oscillating field exhibit a nonequilibrium dynamic phase transition (DPT). The DPT occurs when the field frequency is of the order of the inverse of an intrinsic lifetime associated with the transitions between the two stable states in a static field of the same magnitude as the amplitude of the oscillating field. The DPT is continuous and belongs to the same universality class as the equilibrium phase transition of the Ising model in zero field [G. Korniss et al., Phys. Rev. E 63, 016120 (2001); H. Fujisaka et al., Phys. Rev. E 63, 036109 (2001)]. However, it has previously been claimed that the DPT becomes discontinuous at temperatures below a tricritical point [M. Acharyya, Phys. Rev. E 59, 218 (1999)]. This claim was based on observations in dynamic Monte Carlo simulations of a multipeaked probability density for the dynamic order parameter and negative values of the fourth-order cumulant ratio. Both phenomena can be characteristic of discontinuous phase transitions. Here we use classical nucleation theory for the decay of metastable phases, together with data from large-scale dynamic Monte Carlo simulations of a two-dimensional kinetic Ising ferromagnet, to show that these observations in this case are merely finite-size effects. For sufficiently small systems and low temperatures, the continuous DPT is replaced, not by a discontinuous phase transition, but by a crossover to stochastic resonance. In the infinite-system limit, the stochastic-resonance regime vanishes, and the continuous DPT should persist for all nonzero temperatures.

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PubMed2002

Scaling analysis of a divergent prefactor in the metastable lifetime of a square-lattice Ising ferromagnet at low temperatures.

We examine a square-lattice nearest-neighbor Ising quantum ferromagnet coupled to d-dimensional phonon baths. Using the density-matrix equation, we calculate the transition rates between configurations, which determines the specific dynamic. Applying the calculated stochastic dynamic in Monte Carlo simulations, we measure the lifetimes of the metastable state. As the magnetic field approaches [H]/J=2 at low temperatures, the lifetime prefactor diverges because the transition rates between certain configurations approach zero under these conditions. Near [H]/J=2 and zero temperature, the divergent prefactor shows scaling behavior as a function of the field, temperature, and the dimension of the phonon baths. With proper scaling, the simulation data at different temperatures and for different dimensions of the baths collapse well onto two master curves, one for [H]/J>2 and one for [H]/J<2.

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PubMed2000

Dynamic phase transition, universality, and finite-size scaling in the two-dimensional kinetic Ising model in an oscillating field.

We study the two-dimensional kinetic Ising model below its equilibrium critical temperature, subject to a square-wave oscillating external field. We focus on the multidroplet regime, where the metastable phase decays through nucleation and growth of many droplets of the stable phase. At a critical frequency, the system undergoes a genuine nonequilibrium phase transition, in which the symmetry-broken phase corresponds to an asymmetric stationary limit cycle for the time-dependent magnetization. We investigate the universal aspects of this dynamic phase transition at various temperatures and field amplitudes via large-scale Monte Carlo simulations, employing finite-size scaling techniques adopted from equilibrium critical phenomena. The critical exponents, the fixed-point value of the fourth-order cumulant, and the critical order-parameter distribution all are consistent with the universality class of the two-dimensional equilibrium Ising model. We also study the cross-over from the multidroplet regime to the strong-field regime, where the transition disappears.

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PubMed2000

Microchip electrophoresis: a method for high-speed SNP detection.

As a trial practical application, we have applied optimized microfabricated electrophoresis devices, combined with enzymatic mutation detection methods, to the determination of single nucleotide polymorphism (SNP) sites in the p53 suppressor gene. Using clinical samples, we have achieved robust assays with quality factors as good as conventional electrophoresis in approximately 100 s. This is 10 and 50 times faster than capillary and slab gel electro-phoresis, respectively. The method was highly accurate with an average error of mutation site measurement of only +/-5 bp. No clean-up of the digestion mixtures was needed prior to injection. This greatly simplifies sample handling relative to capillary instruments, which is important for high-throughput screening applications. Following identification, absolute mutation determination of the screened samples was achieved in a second microdevice optimized for four-color DNA sequencing. Total run time was 25 min in this second device and sequencing data were in full agreement with ABI Prism 377 sequencing runs which required 3.5 h. The tandem application of microdevices for location then full characterization of SNPs appears to confirm many of the improvements claimed for future application of microdevices in practical scaled screening for mutational analysis.

DNA Mutational Analysis↗

PubMed1998

Automated fluorescent analysis procedure for enzymatic mutation detection.

The Enzymatic Mutation Detection (EMD) assay detects mutations or polymorphisms in DNA. The assay procedure takes <1 h and is followed by electrophoretic detection. We report an automated procedure, using fluorescently labeled probe and quantitative analysis on the ABI Prism 377 DNA Sequencer, that improves on earlier methods (1, 2) by eliminating the need for sample purification, shortening the hybridization time, and increasing the signal-to-noise ratio. The EMD assay uses the bacteriophage resolvase T4 endonuclease VII, which cleaves the heteroduplex molecules at the mismatch site, forming two shorter fragments that are resolved by gel electrophoresis. Unlike existing mutation techniques, the EMD method uses a single protocol to identify point mutations, deletions, and insertions for all DNA fragments. Test DNA samples are assayed directly from PCR reactions, and fragments up to 4 kb in size have been assayed successfully. A independent analysis on the p53 tumor suppressor gene from clinical samples has shown 100% sensitivity and 94% specificity. Because the fluorescent EMD assay has been optimized for high signal-to-noise ratios, mutations can be identified in mixed samples containing up to a 20-fold excess of normal DNA.

Animals↗