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L. W. Lee

Publications and source records attributed to L. W. Lee.

10 recordsLinked to original sources
arXiv2008

Towards Kinetic Modeling of Global Metabolic Networks with Incomplete Experimental Input on Kinetic Parameters

This is the first report, to our knowledge, on a systematic method for constructing a large scale kinetic metabolic model with incomplete information on kinetic parametersr, and its initial application to the modeling of central metabolism of Methylobacterium extorquens AM1, a methylotrophic and environmental important bacterium, with all necessary constraints. Through a systematic and consistent procedure of finding a set of parameters in the physiological range we overcome an outstanding difficulty in large scale kinetic modeling: the requirement for a massive number of enzymatic reaction parameters. We are able to construct the kinetic model based on general biological considerations and incomplete experimental kinetic parameters. The success of our approach with incompletely input information is guaranteed by two known principles in biology, the robustness of the system and the cooperation among its various parts. (Will be pleased to be informed on other methodologies dealing with same type of problems: aoping@u.washington.edu)

q-bio.MN↗
arXiv2007

A Generic Rate Equation for modeling Enzymatic Reactions under Living Conditions

Based on our experience in kinetic modeling of coupled multiple metabolic pathways we propose a generic rate equation for the dynamical modeling of metabolic kinetics. Its symmetric form makes the kinetic parameters (or functions) easy to relate to values in database and to use in computation. In addition, such form is workable to arbitrary number of substrates and products with different stoichiometry. We explicitly show how to obtain such rate equation exactly for various binding mechanisms. Hence the proposed rate equation is formally rigorous. Various features of such a generic rate equation are discussed. For irreversible reactions, the product inhibition which directly arise from enzymatic reaction is eliminated in a natural way. We also discuss how to include the effects of modifiers and cooperativity.

q-bio.MN↗
arXiv2007

Large-scale Monte Carlo simulations of the isotropic three-dimensional Heisenberg spin glass

We study the Heisenberg spin glass by large-scale Monte Carlo simulations for sizes up to 32^3, down to temperatures below the transition temperature claimed in earlier work. The data for the larger sizes show more marginal behavior than that for the smaller sizes, indicating the lower critical dimension is close to, and possibly equal to three. We find that the spins and chiralities behave in a quite similar manner.

cond-mat.dis-nn↗
arXiv2006

Critical behavior of the three- and ten-state short-range Potts glass: A Monte Carlo study

We study the critical behavior of the short-range p-state Potts spin glass in three and four dimensions using Monte Carlo simulations. In three dimensions, for p = 3, a finite-size scaling analysis of the correlation length shows clear evidence of a transition to a spin-glass phase at T_c = 0.273(5) for a Gaussian distribution of interactions and T_c = 0.377(5) for a bimodal distribution. These results indicate that the lower critical dimension of the 3-state Potts glass is below three. By contrast, the correlation length of the ten-state (p = 10) Potts glass in three dimensions remains small even at very low temperatures and thus shows no sign of a transition. In four dimensions we find that the p = 3 Potts glass with Gaussian interactions has a spin-glass transition at T_c =0.536(3).

cond-mat.dis-nn↗
arXiv2005

Nontrivial critical behavior of the free energy in the two-dimensional Ising spin glass with bimodal interactions

A detailed analysis of Monte Carlo data on the two-dimensional Ising spin glass with bimodal interactions shows that the free energy of the model has a nontrivial scaling. In particular, we show by studying the correlation length that much larger system sizes and lower temperatures are required to see the true critical behavior of the model in the thermodynamic limit. Our results agree with data by Lukic et al. in that the degenerate ground state is separated from the first excited state by an energy gap of 2J.

cond-mat.dis-nn↗
arXiv2005

Defect energy of infinite-component vector spin glasses

We compute numerically the zero temperature defect energy, Delta E, of the vector spin glass in the limit of an infinite number of spin components m, for a range of dimensions 2 <= d <= 5. Fitting to Delta E ~ L^theta, where L is the system size, we obtain: theta = -1.54 (d=2), theta = -1.04 (d=3), theta = -0.67 (d=4) and theta = -0.37 (d=5). These results show that the lower critical dimension, d_l (the dimension where theta changes sign), is significantly higher for m=infinity than for finite m (where 2 < d_l < 3).

cond-mat.dis-nn↗
arXiv2005

Correlation length of the two-dimensional Ising spin glass with bimodal interactions

We study the correlation length of the two-dimensional Edwards-Anderson Ising spin glass with bimodal interactions using a combination of parallel tempering Monte Carlo and a rejection-free cluster algorithm in order to speed up equilibration. Our results show that the correlation length grows ~ exp(2J/T) suggesting through hyperscaling that the degenerate ground state is separated from the first excited state by an energy gap ~4J, as would naively be expected.

cond-mat.dis-nn↗
arXiv2004

Spin glasses in the limit of an infinite number of spin components

We consider the spin glass model in which the number of spin components, m, is infinite. In the formulation of the problem appropriate for numerical calculations proposed by several authors, we show that the order parameter defined by the long-distance limit of the correlation functions is actually zero and there is only "quasi long range order" below the transition temperature. We also show that the spin glass transition temperature is zero in three dimensions.

cond-mat.dis-nn↗
arXiv2004

Correlation Length of the Two-Dimensional Ising Spin Glass with Gaussian Interactions

We study the correlation length of the two-dimensional Ising spin glass with a Gaussian distribution of interactions, using an efficient Monte Carlo algorithm proposed by Houdayer, that allows larger sizes and lower temperatures to be studied than was possible before. We find that the "effective" value of the bulk correlation length exponent νincreases as the temperature is lowered, and, at low temperatures, apparently approaches -1/θ, where θ~ -0.29 is the stiffness exponent obtained at zero temperature. This means scaling is satisfied and earlier results at higher temperatures that find a smaller value for νare affected by corrections to scaling.

cond-mat.dis-nn↗