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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 Hits803Downloads318 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 Hits814Downloads312 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 Hits834Downloads369 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 Hits1353Downloads506 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 Hits1541Downloads596 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 Hits1342Downloads467 Comment 0

8. chinaXiv:201605.00998 [pdf]

Quantifying the sequence-function relation in gene silencing by bacterial small RNAs

Yue Hao; Zhongge J. Zhang; David W. Erickson; Min Huang; Yingwu Huang; Junbai Li; Terence Hwa; hualin shi
Subjects: Physics >> Interdisciplinary Physics and Related Areas of Science and Technology

Sequence-function?relations for?small?RNA (sRNA)-mediated?gene?silencing?were quantified for?the?sRNA RyhB and some of its mRNA targets?in?Escherichia coli. Numerous mutants of RyhB and its targets were generated and their?in?vivo functions characterized at various levels of target and RyhB expression. Although a core complementary region is required for repression?by?RyhB, variations?in?the?complementary sequences of?the?core region gave rise to a continuum of repression strengths, correlated exponentially with?the?computed free energy of RyhB-target duplex formation. Moreover,?sequence?variations?inthe?linker region known to interact with?the?RNA chaperone Hfq also gave rise to a continuum of repression strengths, correlated exponentially with?thecomputed energy cost of keeping?the?linker region open. These results support?the?applicability of?the?thermodynamic model?in?predicting sRNA-mRNA interaction and suggest that sequences at these locations may be used to fine-tune?the?degree of repression. Surprisingly, a truncated RyhB without?the?Hfq-binding region is found to repress multiple targets of?the?wild-type RyhB effectively, both?in?the?presence and absence of Hfq, even though?the?former is required for?the?activity of wild-type RyhB itself. These findings challenge?the?commonly accepted model concerning?the?function?of Hfq?in?gene?silencing-bothin?providing stability to?the?sRNAs and?in?catalyzing?the?target mRNAs to take on active conformations-and raise?the?intriguing question of why many endogenous sRNAs subject their functions to Hfq-dependences.

submitted time 2016-05-08 Hits1505Downloads537 Comment 0

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