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1. chinaXiv:201605.01010 [pdf]

Droplets of 3He–4He mixtures

hualin shi; s.t. chui
Subjects: Physics >> Condensed Matter: Structural, Mechanical and Thermal Properties

We study the properties of?3He–4He mixture droplets using a phenomenological density functional. The structure of a liquid drop with and without vortices is investigated using Monte Carlo simulations.

submitted time 2016-05-08 Hits812Downloads325 Comment 0

2. chinaXiv:201605.01009 [pdf]

Droplets of mixtures of he3-he4 at finite vorticity

hualin shi; s.t. chui
Subjects: Physics >> Condensed Matter: Structural, Mechanical and Thermal Properties

Stimulated by recent interests in mixtures of quantum fluids, we study the properties of 3He–4He mixture droplets using a phenomenological density functional. The structure of liquid drop with and without vortices is investigated using Monte Carlo simulations.

submitted time 2016-05-08 Hits819Downloads315 Comment 0

3. chinaXiv:201605.01007 [pdf]

Theoretical studies on sRNA-mediated regulation in bacteria

xiaoxue chang; liufang xu; hualin shi
Subjects: Physics >> General Physics: Statistical and Quantum Mechanics, Quantum Information, etc.

Small RNA(sRNA)-mediated?post-transcriptional?regulation?differs from protein-mediated?regulation. Through base-pairing,?sRNA?can regulate the target mRNAin?a catalytic or stoichiometric manner. Some?theoretical?models were built for comparison of the protein-mediated?and?sRNA-mediated?modes?in?the steady-state behaviors and noise properties. Many experiments demonstrated that a single?sRNA?can regulate several mRNAs, which causes crosstalk between the targets. Here, we focus?on?some models?in?which two target mRNAs are silenced by the same?sRNA?to discuss their crosstalk features. Additionally, the sequence-function relationship of?sRNA?and its role?in?the kinetic process of base-pairing have been highlighted?in?model building.

submitted time 2016-05-08 Hits844Downloads375 Comment 0

4. chinaXiv:201605.01005 [pdf]

The effect of mechanical tension on DNA polymerase activity studied with a two-state model

yaogen shu; hualin shi
Subjects: Physics >> Interdisciplinary Physics and Related Areas of Science and Technology

Single-molecule experiments revealed that?the?replication rate?of?T7?DNA?polymerase?has?a?peak value at?tension?of?about 5.5 pN. However,?the?mechanism leading to this peak has only been partially investigated. Here, we present?a?two-state model to investigate?the?effect?of?mechanical?tension?on?DNApolymerase?activity.?The?model consists?of?polymerase?and exonuclease.?The?polymerase's kinetic pathway has been simplified into Michaelis-Menten formwith?two steps. One is?the?conformational change from "open" to "close".?The?other is?the?base-stacking.?The?results are in good agreement?with?experimental observations. We also predict that?the?tension?on?template is beneficial to?the?fidelity?of?DNA?replication.

submitted time 2016-05-08 Hits1360Downloads509 Comment 0

6. chinaXiv:201605.01003 [pdf]

Theoretical Analysis of Catalytic-sRNA-Mediated Gene Silencing

Yue Hao; fangliu xu; hualin shi
Subjects: Physics >> Interdisciplinary Physics and Related Areas of Science and Technology

Small regulatory RNA (sRNA) that acts by an antisense mechanism is critical for gene regulation at the posttranscriptional level. Recently, an Hfq-dependent sRNA named MicM, which is related to the regulation of outer membrane protein, was verified as a novel antisense sRNA due to its catalytic mode of regulation. Here we propose a simple kinetic model for the enzyme-like regulation mode of sRNA and study in detail the noise properties of the target gene under various recycling rates of the regulator. We predict that the recycling rate of sRNA and other relative parameters have significant influence on the noise strength of target expression. In comparison with the stoichiometric regulatory mode, a lesser fluctuation of target expression was observed near the threshold at which the transcription rates of both sRNA and target mRNA equal each other. We also found that the new mode is better in terms of rapid response to external signals. However, it needs more time to achieve target recovery if the stimulating signal disappears. Additionally, the obtained time evolution results of the MicM-ybfM interaction system based on our model are consistent with previous experimental results, serving as experimental evidence to back up our theoretical analysis. (C) 2010 Elsevier Ltd. All rights reserved.

submitted time 2016-05-08 Hits1547Downloads599 Comment 0

7. chinaXiv:201605.01002 [pdf]

Cooperative effects on the kinetics of ATP hydrolysis in collective molecular motors

yaogen shu; hualin shi
Subjects: Physics >> Interdisciplinary Physics and Related Areas of Science and Technology

Within the framework of a two-state ratchet model, cooperative effects of collective molecular motors on the kinetics of adenosine triphosphate (ATP) hydrolysis have been studied in detail. We calculate the dependence of the rate of ATP consumption on the applied load. Features different from a single molecular motor have been found. We analyze two typical oscillations of collective molecular motors. The relations between the ATP concentration and oscillatory characteristics, such as frequency, amplitude, and the duty ratio, have been discussed.

submitted time 2016-05-08 Hits1352Downloads473 Comment 0

8. chinaXiv:201605.01001 [pdf]

Temperature-dependent frequency shifts in collective excitations of a Bose-Einstein condensate

Hualin Shi; Wei-Mou Zheng
Subjects: Physics >> Condensed Matter: Structural, Mechanical and Thermal Properties

By including the contribution of the thermal cloud in the Lagrangian of the condensate of a Bose gas, we extend the time-dependent variational method at zero temperature to study temperature-dependent low collective excitation modes. A Gaussian trial wave function of the condensate and a static distribution density of the thermal cloud are used and analytical expressions for temperature-dependent excitation frequencies obtained. Theoretical results are compared with measurements in the JILA and MIT experiments.

submitted time 2016-05-08 Hits1045Downloads407 Comment 0

9. chinaXiv:201605.01000 [pdf]

Phase separation of Bose gases at finite temperature

Hualin Shi; Wei-Mou Zheng; Siu-Tat Chui
Subjects: Physics >> Condensed Matter: Structural, Mechanical and Thermal Properties

Phase separation of two-component untrapped and trapped Bose gases at finite temperature is studied. Conditions for the stability of a homogeneous binary Bose gas mixture at finite temperature and the density profile of the trapped binary mixture are obtained. Our extended results include the known results for zero temperature.

submitted time 2016-05-08 Hits1068Downloads413 Comment 0

10. chinaXiv:201605.00999 [pdf]

Thermodynamic Properties of a Trapped Interacting Bose Gas

Hualin Shi; Wei-Mou Zheng
Subjects: Physics >> Condensed Matter: Structural, Mechanical and Thermal Properties

A Bose gas in an external potential is studied by means of the local density approximation. Analytical results are derived for the thermodynamic properties of an ideal Bose gas in a generic power-law trapping potential, and their dependence on the mutual interaction of atoms in the case of a non-ideal Bose gas.

submitted time 2016-05-08 Hits1040Downloads389 Comment 0

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