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L. Yin

Publications and source records attributed to L. Yin.

32 records · Page 2Linked 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↗
arXiv2008

Universal Scaling of Pinning Effect on Hall Anomaly near the Vortex Glass Transition and Doping Dependence Problems of Superconductors

We find universal scaling relations of the pinning effect on the Hall resistivity $ρ_{xy}$ and Hall angle $θ_{H}$. Considering the extended power law form of $ρ_{xx}$ and the microscopic analysis of $σ_{xy}$, we obtain unified $ρ_{xy}$ equations for superconductors with and without double sign reversal. These equations reasonably explain the striking universality in doping dependence found by Nagoaka et al., which contradicts the prediction of the time dependent Ginzburg-Landau equation based on s-wave coupling theory [PRL {\bf{80}},3594 (1998)]. A full comparison of experiment with prediction from theoretical models is proposed.

cond-mat.supr-con↗
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

Langmuir wave filamentation instability

A Langmuir wave (LW) model is constructed whose equilibria are consistent with stimulated Raman scatter optimization, with Hamiltonian dynamics and with rotational invariance. Linear instability analysis includes terms to all orders in wave amplitude and fluctuation wavenumber expansions, deltak. Resultant LW modulational instability is nonstandard: as the LW amplitude increases, unstable deltak range first expands and then shrinks to zero. Large amplitude wave model dynamics requires hyper-diffraction terms if k LambdaD < 0.45, lest artificially small length scales become unstable.

physics.plasm-ph↗
arXiv2006

Efficiency, Robustness and Stochasticity of Gene Regulatory Networks in Systems Biology: lambda Switch as a Working Example

Phage lambda is one of the most studied biological models in modern molecular biology. Over the past 50 years quantitative experimental knowledge on this biological model has been accumulated at all levels: physics, chemistry, genomics, proteomics, functions, and more. All its components have been known to a great detail. The theoretical task has been to integrate its components to make the organism working quantitatively in a harmonic manner. This would test our biological understanding and would lay a solid fundamental for further explorations and applications, an obvious goal of systems biology. One of the outstanding challenges in doing so has been the so-called stability puzzle of lambda switch: the biologically observed robustness and its difficult mathematical reconstruction based on known experimental values. In this chapter we review the recent theoretical and experimental efforts on tackling this problem. An emphasis is put on the minimum quantitative modeling where a successful numerical agreement between experiments and modeling has been achieved. A novel method tentatively named stochastic dynamical structure analysis emerged from such study is also discussed within a broad modeling perspective.

q-bio.SC↗
arXiv2005

Scaling of Nonlinear Longitudinal and Hall Resistivities near the Vortex Glass Transition

We show that the longitudinal current-voltage characteristics of superconductors in mixed state have the general form of extended power law. Isotherms simulated from this nonlinear equation fit the experimental I-V data of Strachan et al. [ Phys. Rev. Lett. {\bf 87}, 067007 (2001)]. We determine the average pinning force in the flux creep and strong pinning regime and discuss both the puzzling scaling behavior $ρ_{xy}\proptoρ_{xx}^β$ and a recently found new scaling relationship of nonlinear Hall resistivity $ρ_{xy}(T)$.

cond-mat.supr-con↗
arXiv2004

Limit Cycle and Conserved Dynamics

We demonstrate that a potential coexists with limit cycle. Here the potential determines the final distribution of population. Our demonstration consists of three steps: We first show the existence of limit from a typical physical sciences setting: the potential is a type of Mexican hat type, with the strength of a magnetic field scale with the strength the potential gradient near the limit cycle, and the friction goes to zero faster than the potential near the limit cycle. Hence the dynamics at the limit cycle is conserved. The diffusion matrix is nevertheless finite at the limit cycle. Secondly, we construct the potential in the dynamics with limit cycle in a typical dynamical systems setting. Thirdly, we argue that such a construction can be carried out in a more general situation based on a method discovered by one of us. This method of dealing with stochastic differential equation is in general different from both Ito and Stratonovich calculus. Our result may be useful in many related applications, such as in the discussion of metastability of limit cycle and in the construction of Hopfield potential in the neural network computation.

nlin.CD↗
arXiv2004

Critical Scaling of Extended Power Law I-V Isotherms near Vortex Glass Transition

In view of the question about the vortex glass theory of the freezing of disordered vortex matter raised by recent experimental observations we reinvestigate the critical scaling of high $T_c$ superconductors. We find that dc current-voltage characteristic of mixed state superconductors has the general form of extended power law which is based on the Ginzburg-Landau (GL) functional in the similar way as the vortex glass theory. Isotherms simulated from this nonlinear equation fit the experimental I-V data of Strachan et al.[Phys.Rev.Lett. 87, 067007 (2001)]. The puzzling question of the derivative plot for the I-V curves and the controversy surrounding the values of critical exponents are also discussed.

cond-mat.supr-con↗
arXiv2004

Robustness, Stability and Efficiency of Phage lambda Gene Regulatory Network: Dynamical Structure Analysis

Based on our physical and biological studies we have recently developed a mathematical framework for the analysis of nonlnear dynamics. We call this framework the dynamical structure analysis. It has four dynamical elements: potential landscape, transverse matrix, descendant matrix, and stochastic drive. In particular, the importance and the existence of the potential landscape is emphasized. The dynamical structure analysis is illustrated in detail by the study of stability, robustness, and efficiency of the simplest gene regulatory network of phage lambda.

q-bio.MN↗
arXiv2004

Calculating Biological Behaviors of Epigenetic States in Phage lambda Life Cycle

Gene regulatory network of lambda phage is one the best studied model systems in molecular biology. More 50 years of experimental study has provided a tremendous amount of data at all levels: physics, chemistry, DNA, protein, and function. However, its stability and robustness for both wild type and mutants has been a notorious theoretical/mathematical problem. In this paper we report our successful calculation on the properties of this gene regulatory network. We believe it is of its first kind. Our success is of course built upon numerous previous theoretical attempts, but following 3 features make our modeling uniqu: 1) A new modeling method particular suitable for stability and robustness study; 2) Paying a close attention to the well-known difference of in vivo and in vitro; 3) Allowing more important role for noise and stochastic effect to play. The last two points have been discussed by two of us (Ao and Yin, cond-mat/0307747), which we believe would be enough to make some of previous theoretical attempts successful, too. We hope the present work would stimulate a further interest in the emerging field of gene regulatory network.

q-bio.MN↗
arXiv2004

Surface plasmons at single nanoholes in Au-films

The generation of surface plasmon polaritons (SPP's) at isolated nanoholes in 100 nm thick Au films is studied using near-field scanning optical microscopy (NSOM). Finite-difference time-domain calculations, some explicitly including a model of the NSOM tip, are used to interpret the results. We find the holes act as point-like sources of SPP's and demonstrate that interference between SPP's and a directly transmitted wave allows for determination of the wavelength, phase, and decay length of the SPP. The near-field intensity patterns can be manipulated by varying the angle and polarization of the incident beam.

cond-mat.mtrl-sci↗
arXiv2003

Towards the Understanding of Stability Puzzles in Phage lambda

We discuss two aspects, the in vivo and in vitro difference and the modeling of noise, of integrative modeling of network dynamics in biology, using phage lambda as an example. We believe those two aspects have not been seriously considered, and the including of them may be enough to solve the outstanding stability and robustness puzzle of in gene regulatory network dynamics.

cond-mat.soft↗
arXiv1995

Spectral Anomaly and High Temperature Superconductors

Spectral anomaly for interacting Fermions is characterized by the spectral function $A([k-k_F],ω)$ satisfying the scaling relation $A(Λ^{y_1} [k-k_F],Λ^{y_2}ω)= Λ^{y_A}A([k-k_F],ω)$, where $y_1$, $y_2$, and $y_A$ are the exponents defining the universality class. For a Fermi liquid $y_1=1$, $y_2=1$, $y_A=-1$; all other values of the exponents are termed anomalous. In this paper, an example for which $y_1=1$, $y_2=1$, but $y_A=α-1$ is considered in detail. Attractive interaction added to such a critical system leads to a novel superconducting state, which is explored and its relevance to high temperature cuprate superconductors is discussed.

cond-mat↗