Subjects: Physics >> Condensed Matter: Structural, Mechanical and Thermal Properties submitted time 2016-05-08
Abstract: 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.
Peer Review Status:Awaiting Review
Subjects: Physics >> Condensed Matter: Structural, Mechanical and Thermal Properties submitted time 2016-05-08
Abstract: 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.
Peer Review Status:Awaiting Review
Subjects: Physics >> General Physics: Statistical and Quantum Mechanics, Quantum Information, etc. submitted time 2016-05-08
Abstract: Small RNA(sRNA)-mediated爌ost-transcriptional爎egulation燿iffers from protein-mediated爎egulation. Through base-pairing,爏RNA燾an regulate the target mRNAin燼 catalytic or stoichiometric manner. Some爐heoretical爉odels were built for comparison of the protein-mediated燼nd爏RNA-mediated爉odes爄n爐he steady-state behaviors and noise properties. Many experiments demonstrated that a single爏RNA燾an regulate several mRNAs, which causes crosstalk between the targets. Here, we focus爋n爏ome models爄n爓hich two target mRNAs are silenced by the same爏RNA爐o discuss their crosstalk features. Additionally, the sequence-function relationship of爏RNA燼nd its role爄n爐he kinetic process of base-pairing have been highlighted爄n爉odel building.
Peer Review Status:Awaiting Review
Subjects: Physics >> Interdisciplinary Physics and Related Areas of Science and Technology submitted time 2016-05-08
Abstract: Single-molecule experiments revealed that爐he爎eplication rate爋f燭7燚NA爌olymerase爃as燼爌eak value at爐ension爋f燼bout 5.5 pN. However,爐he爉echanism leading to this peak has only been partially investigated. Here, we present燼爐wo-state model to investigate爐he爀ffect爋f爉echanical爐ension爋n燚NApolymerase燼ctivity.燭he爉odel consists爋f爌olymerase燼nd exonuclease.燭he爌olymerase's kinetic pathway has been simplified into Michaelis-Menten formwith爐wo steps. One is爐he燾onformational change from "open" to "close".燭he爋ther is爐he燽ase-stacking.燭he爎esults are in good agreement爓ith爀xperimental observations. We also predict that爐he爐ension爋n爐emplate is beneficial to爐he爁idelity爋f燚NA爎eplication.
Peer Review Status:Awaiting Review
Subjects: Physics >> Interdisciplinary Physics and Related Areas of Science and Technology submitted time 2016-05-08
Abstract: Cell cycle;燫eplication initiation;燙ell growth;燚naA;燫NA polymerase
Peer Review Status:Awaiting Review
Subjects: Physics >> Interdisciplinary Physics and Related Areas of Science and Technology submitted time 2016-05-08
Abstract: 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.
Peer Review Status:Awaiting Review
Subjects: Physics >> Interdisciplinary Physics and Related Areas of Science and Technology submitted time 2016-05-08
Abstract: 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.
Peer Review Status:Awaiting Review
Subjects: Physics >> Interdisciplinary Physics and Related Areas of Science and Technology submitted time 2016-05-08
Abstract: Sequence-function爎elations for爏mall燫NA (sRNA)-mediated爂ene爏ilencing爓ere quantified for爐he爏RNA RyhB and some of its mRNA targets爄n燛scherichia coli. Numerous mutants of RyhB and its targets were generated and their爄n爒ivo functions characterized at various levels of target and RyhB expression. Although a core complementary region is required for repression燽y燫yhB, variations爄n爐he燾omplementary sequences of爐he燾ore region gave rise to a continuum of repression strengths, correlated exponentially with爐he燾omputed free energy of RyhB-target duplex formation. Moreover,爏equence爒ariations爄nthe爈inker region known to interact with爐he燫NA chaperone Hfq also gave rise to a continuum of repression strengths, correlated exponentially with爐hecomputed energy cost of keeping爐he爈inker region open. These results support爐he燼pplicability of爐he爐hermodynamic model爄n爌redicting sRNA-mRNA interaction and suggest that sequences at these locations may be used to fine-tune爐he燿egree of repression. Surprisingly, a truncated RyhB without爐he燞fq-binding region is found to repress multiple targets of爐he爓ild-type RyhB effectively, both爄n爐he爌resence and absence of Hfq, even though爐he爁ormer is required for爐he燼ctivity of wild-type RyhB itself. These findings challenge爐he燾ommonly accepted model concerning爐he爁unction爋f Hfq爄n爂ene爏ilencing-bothin爌roviding stability to爐he爏RNAs and爄n燾atalyzing爐he爐arget mRNAs to take on active conformations-and raise爐he爄ntriguing question of why many endogenous sRNAs subject their functions to Hfq-dependences.
Peer Review Status:Awaiting Review