arXiv subjects

Lei-Han Tang

Publications and source records attributed to Lei-Han Tang.

At least 37 records · Page 2Linked to original sources

arXiv2009

Attenuation of transcriptional bursting in mRNA transport

Due to the stochastic nature of biochemical processes, the copy number of any given type of molecule inside a living cell often exhibits large temporal fluctuations. Here, we develop analytic methods to investigate how the noise arising from a bursting input is reshaped by a transport reaction which is either linear or of the Michaelis-Menten type. A slow transport rate smoothes out fluctuations at the output end and minimizes the impact of bursting on the downstream cellular activities. In the context of gene expression in eukaryotic cells, our results indicate that transcriptional bursting can be substantially attenuated by the transport of mRNA from nucleus to cytoplasm. Saturation of the transport mediators or nuclear pores contributes further to the noise reduction. We suggest that the mRNA transport should be taken into account in the interpretation of relevant experimental data on transcriptional bursting.

q-bio.SC↗

arXiv2009

Topological glass states

In connection with recent discussion of topological order and topological phase transitions in quantum systems, we reexamine circumstances that lead to the appearance of a topological glass in certain classical lattice spin models. Local bonding enforces constraints on low energy states which organize themselves into topologically distinct classes that break ergodicity but not any apparent symmetry as in the usual Landau theory of phase transitions. Various properties of such a topological glass are demonstrated using two classical Ising-like models.

cond-mat.stat-mech↗

arXiv2008

Coordination motifs and large-scale structural organization in atomic clusters

The structure of nanoclusters is complex to describe due to their noncrystallinity, even though bonding and packing constraints limit the local atomic arrangements to only a few types. A computational scheme is presented to extract coordination motifs from sample atomic configurations. The method is based on a clustering analysis of multipole moments for atoms in the first coodination shell. Its power to capture large-scale structural properties is demonstrated by scanning through the ground state of the Lennard-Jones and C$_{60}$ clusters collected at the Cambridge Cluster Database.

cond-mat.mtrl-sci↗

arXiv2008

Phase glass and zero-temperature phase transition in a randomly frustrated two-dimensional quantum rotor model

The ground state of the quantum rotor model in two dimensions with random phase frustration is investigated. Extensive Monte Carlo simulations are performed on the corresponding (2+1)-dimensional classical model under the entropic sampling scheme. For weak quantum fluctuation, the system is found to be in a phase glass phase characterized by a finite compressibility and a finite value for the Edwards-Anderson order parameter, signifying long-ranged phase rigidity in both spatial and imaginary time directions. Scaling properties of the model near the transition to the gapped, Mott insulator state with vanishing compressibility are analyzed. At the quantum critical point, the dynamic exponent $z_{\rm dyn}\simeq 1.17$ is greater than one. Correlation length exponents in the spatial and imaginary time directions are given by $ν\simeq 0.73$ and $ν_z\simeq 0.85$, respectively, both assume values greater than 0.6723 of the pure case. We speculate that the phase glass phase is superconducting rather than metallic in the zero current limit.

cond-mat.supr-con↗

arXiv2007

Entrainment transition in populations of random frequency oscillators

The entrainment transition of coupled random frequency oscillators is revisited. The Kuramoto model (global coupling) is shown to exhibit unusual sample-dependent finite size effects leading to a correlation size exponent $\barν=5/2$. Simulations of locally coupled oscillators in $d$-dimensions reveal two types of frequency entrainment: mean-field behavior at $d>4$, and aggregation of compact synchronized domains in three and four dimensions. In the latter case, scaling arguments yield a correlation length exponent $ν=2/(d-2)$, in good agreement with numerical results.

cond-mat.stat-mech↗

arXiv2007

Finite-size scaling of synchronized oscillation on complex networks

The onset of synchronization in a system of random frequency oscillators coupled through a random network is investigated. Using a mean-field approximation, we characterize sample-to-sample fluctuations for networks of finite size, and derive the corresponding scaling properties in the critical region. For scale-free networks with the degree distribution $P(k)\sim k^{-γ}$ at large $k$, we found that the finite size exponent $\barν$ takes on the value 5/2 when $γ>5$, the same as in the globally coupled Kuramoto model. For highly heterogeneous networks ($3<γ<5$), $\barν$ and the order parameter exponent $β$ depend on $γ$. The analytic expressions for these exponents obtained from the mean field theory are shown to be in excellent agreement with data from extensive numerical simulations.

cond-mat.stat-mech↗

arXiv2006

Anomalous Binder Cumulant and Lack of Self-Averageness in Systems with Quenched Disorder

The Binder cumulant (BC) has been widely used for locating the phase transition point accurately in systems with thermal noise. In systems with quenched disorder, the BC may show subtle finite-size effects due to large sample-to-sample fluctuations. We study the globally coupled Kuramoto model of interacting limit-cycle oscillators with random natural frequencies and find an anomalous dip in the BC near the transition. We show that the dip is related to non-self-averageness of the order parameter at the transition. Alternative definitions of the BC, which do not show any anomalous behavior regardless of the existence of non-self-averageness, are proposed.

cond-mat.stat-mech↗

arXiv2006

Ground state and glass transition of the RNA secondary structure

RNA molecules form a sequence-specific self-pairing pattern at low temperatures. We analyze this problem using a random pairing energy model as well as a random sequence model that includes a base stacking energy in favor of helix propagation. The free energy cost for separating a chain into two equal halves offers a quantitative measure of sequence specific pairing. In the low temperature glass phase, this quantity grows quadratically with the logarithm of the chain length, but it switches to a linear behavior of entropic origin in the high temperature molten phase. Transition between the two phases is continuous, with characteristics that resemble those of a disordered elastic manifold in two dimensions. For designed sequences, however, a power-law distribution of pairing energies on a coarse-grained level may be more appropriate. Extreme value statistics arguments then predict a power-law growth of the free energy cost to break a chain, in agreement with numerical simulations. Interestingly, the distribution of pairing distances in the ground state secondary structure follows a remarkable power-law with an exponent -4/3, independent of the specific assumptions for the base pairing energies.

q-bio.BM↗

arXiv2004

Zero-temperature criticality in the two-dimensional gauge glass model

The zero-temperature critical state of the two-dimensional gauge glass model is investigated. It is found that low-energy vortex configurations afford a simple description in terms of gapless, weakly interacting vortex-antivortex pair excitations. A linear dielectric screening calculation is presented in a renormalization group setting that yields a power-law decay of spin-wave stiffness with distance. These properties are in agreement with low-temperature specific heat and spin-glass susceptibility data obtained in large-scale multi-canonical Monte Carlo simulations.

cond-mat.dis-nn↗

arXiv2004

Directional Ordering of Fluctuations in a Two-dimensional Compass Model

In the Mott insulating phase of the transition metal oxides, the effective orbital-orbital interaction is directional both in the orbital space and in the real space. We discuss a classical realization of directional coupling in two dimensions. Despite extensive degeneracy of the ground state, the model exhibits partial orbital ordering in the form of directional ordering of fluctuations at low temperatures stabilized by an entropy gap. Transition to the disordered phase is shown to be in the Ising universality class through exact mapping and multicanonical Monte Carlo simulations.

cond-mat.str-el↗

arXiv2001

Anomalous finite-size effect in superconducting Josephson junction arrays

We report large-scale simulations of the resistively-shunted Josephson junction array in strip geometry. As the strip width increases, the voltage first decreases following the dynamic scaling ansatz proposed by Minnhagen {\it et al.} [Phys. Rev. Lett. {\bf 74}, 3672 (1995)], and then rises towards the asymptotic value predicted by Ambegaokar {\it et al.} [Phys. Rev. Lett. {\bf 40}, 783 (1978)]. The nonmonotonic size-dependence is attributed to shortened life time of free vortices in narrow strips, and points to the danger of single-scale analysis applied to a charge-neutral superfluid state.

cond-mat.stat-mech↗

arXiv2000

Rare-event induced binding transition of heteropolymers

Sequence heterogeneity broadens the binding transition of a polymer onto a linear or planar substrate. This effect is analyzed in a real-space renormalization group scheme designed to capture the statistics of rare events. In the strongly disordered regime, binding initiates at an exponentially rare set of ``good contacts''. Renormalization of the contact potential yields a Kosterlitz-Thouless type transition in any dimension. This and other predictions are confirmed by extensive numerical simulations of a directed polymer interacting with a columnar defect.

cond-mat.stat-mech↗

arXiv2000

Modelling High-frequency Economic Time Series

The minute-by-minute move of the Hang Seng Index (HSI) data over a four-year period is analysed and shown to possess similar statistical features as those of other markets. Based on a mathematical theorem [S. B. Pope and E. S. C. Ching, Phys. Fluids A {\bf 5}, 1529 (1993)], we derive an analytic form for the probability distribution function (PDF) of index moves from fitted functional forms of certain conditional averages of the time series. Furthermore, following a recent work by Stolovitzky and Ching, we show that the observed PDF can be reproduced by a Langevin process with a move-dependent noise amplitude. The form of the Langevin equation can be determined directly from the market data.

cond-mat.stat-mech↗

arXiv2000

Superconducting correlations in ultra-small metallic grains

To describe the crossover from the bulk BCS superconductivity to a fluctuation-dominated regime in ultrasmall metallic grains, new order parameters and correlation functions, such as ``parity gap'' and ``pair-mixing correlation function'', have been recently introduced. In this paper, we discuss the small-grain behaviour of the Penrose-Onsager-Yang off-diagonal long-range order (ODLRO) parameter in a pseudo-spin representation. Relations between the ODLRO parameter and those mentioned above are established through analytical and numerical calculations.

cond-mat.supr-con↗

arXiv1998

Reaction-Diffusion-Branching Models of Stock Price Fluctuations

Several models of stock trading [P. Bak et al, Physica A {\bf 246}, 430 (1997)] are analyzed in analogy with one-dimensional, two-species reaction-diffusion-branching processes. Using heuristic and scaling arguments, we show that the short-time market price variation is subdiffusive with a Hurst exponent $H=1/4$. Biased diffusion towards the market price and blind-eyed copying lead to crossovers to the empirically observed random-walk behavior ($H=1/2$) at long times. The calculated crossover forms and diffusion constants are shown to agree well with simulation data.

cond-mat.stat-mech↗

arXiv1998

Comment on ``Nonuniversal Exponents in Interface Growth''

Recently, Newman and Swift[T. J. Newman and M. R. Swift, Phys. Rev. Lett. {\bf 79}, 2261 (1997)] made an interesting suggestion that the strong-coupling exponents of the Kardar-Parisi-Zhang (KPZ) equation may not be universal, but rather depend on the precise form of the noise distribution. We show here that the decrease of surface roughness exponents they observed can be attributed to a percolative effect.

cond-mat.stat-mech↗

arXiv1998

Unstable Growth and Coarsening in Molecular-Beam Epitaxy

The coarsening dynamics of three-dimensional islands on a growing film is discussed. It is assumed that the origin of the initial instability of a planar surface is the Ehrlich-Schwoebel step-edge barrier for adatom diffusion. Two mechanisms of coarsening are identified: (i) surface diffusion driven by an uneven distribution of bonding energies, and (ii) mound coalescence driven by random deposition. Semiquantitative estimates of the coarsening time are given in each case. When the surface slope saturates, an asymptotic dynamical exponent $z=4$ is obtained.

cond-mat.stat-mech↗

arXiv1998

Parity effect in a small superconducting grain: A rigorous result

The parity effect in an ultra-small superconducting grain is examined. By applying a generalized version of Lieb's spin-reflection positivity technique, we show rigorously that the parity parameter $Δ_P$ is nonvanishing in such a system. A positive lower bound for $Δ_P$ is derived.

cond-mat.supr-con↗