Biomedical subjects

Zhi-Jie Tan

Publications and source records attributed to Zhi-Jie Tan.

6 recordsLinked to original sources

PubMed2026

Multivalent cations stabilize DNA duplexes beyond charge neutralization.

Multivalent cations are abundant in cells and play essential roles in DNA duplex stability, genome packaging, and DNA-protein interactions. They can also condense DNA, making it challenging to determine their influence on DNA duplex stability. To overcome this challenge, we studied DNA unpeeling at equilibrium under high tension using magnetic tweezers, thereby preventing condensation. Experiments show that DNA duplex stability first increases and then decreases as cation concentration increases and the maximum DNA duplex stability increases with cation valence. The maximum free energy change of DNA was 3.33 k B T/bp for Na+ and increased to 3.98 k B T/bp for protamine, which is a small arginine-rich protein with a highly positive charge (≈21 for salmon sperm), corresponding to a relative increase of 19.5%. Consistently, all-atom molecular dynamics simulations show that higher-valent cations preferentially embed in the minor groove of DNA and clamp the minor groove, in contrast to the major-groove clamping reported for RNA, thereby stabilizing the helix more efficiently. These findings establish a single-molecule framework for quantifying DNA thermodynamics in complex ionic environments, which contributes to understanding ionic control of genome stability and to designing ion-tunable DNA-based nanostructures and delivery systems.

Journal Article↗

PubMed2003

Critical behavior of efficiency dynamics in small-world networks.

Some dynamical processes in a small-world network shows a critical transition at a finite disorder phi(c) of the network, in contrast with the geometrical properties that exhibit the critical behavior at phi(c)=0. Although it has been pointed out in previous works that the transition is related to the structural properties of the network, it is still not very clear why the transition occurs at phi(c) not equal 0. In this paper we present a simple social model of efficiency dynamics in small-world networks, which also shows a transition at phi(c)>0. We obtain the critical point with phi(c) approximately equal 0.098 from the finite-size analysis. It is found that both the geometrical properties of the network and the specific dynamical characters of the model contribute to the critical transition. This work is useful for understanding this kind of transition occurring in many dynamical processes in small-world networks.

Journal Article↗

PubMed2003

Network-induced nonequilibrium phase transition in the "game of Life".

A cellular automation model of the "game of Life" on a two-dimensional small-world network is presented in order to count in long-range interactions among living individuals in social or biological systems. The density of the life and its fluctuation are calculated, respectively. The present model exhibits a nonequilibrium phase transition from an "inactive-sparse" state to an "active-dense" one at a certain intermediate value of the network disorder. Employing finite-size scaling analysis, we estimate the location of the critical point with p(c)( infinity ) approximately 0.3685. The transition is of the "second-order" type with power-law diverging length. We obtain the critical exponents 1/nu approximately 1.70, beta approximately 0.50, and beta/nu approximately 0.85. The calculated results indicate that the present model may belong to the universality class of directed percolation.

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PubMed2002

Patterns of particle distribution in multiparticle systems by random walks with memory enhancement and decay.

We investigate the pattern of particle distribution and its evolution with time in multiparticle systems using the model of random walks with memory enhancement and decay. This model describes some biological intelligent walks. With decrease in the memory decay exponent alpha, the distribution of particles changes from a random dispersive pattern to a locally dense one, and then returns to the random one. Correspondingly, the fractal dimension D(f,p) characterizing the distribution of particle positions increases from a low value to a maximum and then decreases to the low one again. This is determined by the degree of overlap of regions consisting of sites with remanent information. The second moment of the density rho(2) was introduced to investigate the inhomogeneity of the particle distribution. The dependence of rho(2) on alpha is similar to that of D(f,p) on alpha. rho(2) increases with time as a power law in the process of adjusting the particle distribution, and then rho(2) tends to a stable equilibrium value.

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PubMed2002

Pattern formation on nonuniform surfaces by correlated random sequential absorptions.

The pattern formation on nonuniform surfaces by correlated-random sequential absorption (CRSA) process has been investigated by computer simulations. The nonuniform surfaces are represented by percolation clusters with probabilities p(s) and p(s) stands for the nonuniform degree of surfaces. The interactions between the particles and the defects in surfaces are involved by introducing a sticking coefficient s. When s-->0, the CRSA process is controlled by the absorption of surfaces and the correlation between particles. With the correlation increasing from a weak limit to a strong one, the cluster consisting of absorbed particles changes from the dispersed pattern of site percolation to correlated percolation, and then to Leath percolation clusters. When s-->1 and p(s)-->p(c), the CRSA process is dominated by the absorption of the defects, where p(c) is the threshold of percolations. The patterns appear randomly dispersed in spite of the correlation. With the decrease of s and increase of p(s), the interaction controlling the CRSA process changes from the absorption of defects to that of surface and the correlation between particles gradually. For the system s-->0, the transition correlation exponent alpha(c)=d(s), where d(s) is the fractal dimension of the percolation surfaces.

Journal Article↗

PubMed2002

Random walk with memory enhancement and decay.

A model of random walk with memory enhancement and decay was presented on the basis of the characteristics of the biological intelligent walks. In this model, the movement of the walker is determined by the difference between the remaining information at the jumping-out site and jumping-in site. The amount of the memory information s(i)(t) at a site i is enhanced with the increment of visiting times to that site, and decays with time t by the rate e(-beta(t)), where beta is the memory decay exponent. When beta=0, there exists a transition from Brownian motion (BM) to the compact growth of walking trajectory with the density of information energy u increasing. But for beta>0, this transition does not appear and the walk with memory enhancement and decay can be considered as the BM of the mass center of the cluster composed of remembered sites in the late stage.

Animals↗