分类: 物理学 >> 凝聚态:结构、力学和热性能 提交时间: 2016-05-08
摘要: 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.
分类: 物理学 >> 凝聚态:结构、力学和热性能 提交时间: 2016-05-08
摘要: 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.
分类: 物理学 >> 普通物理:统计和量子力学,量子信息等 提交时间: 2016-05-08
摘要: 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.
分类: 物理学 >> 交叉学科物理及相关领域的科学与技术 提交时间: 2016-05-08
摘要: 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.
分类: 物理学 >> 交叉学科物理及相关领域的科学与技术 提交时间: 2016-05-08
摘要: Cell cycle; Replication initiation; Cell growth; DnaA; RNA polymerase
分类: 物理学 >> 交叉学科物理及相关领域的科学与技术 提交时间: 2016-05-08
摘要: 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.
分类: 物理学 >> 交叉学科物理及相关领域的科学与技术 提交时间: 2016-05-08
摘要: 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.
分类: 物理学 >> 交叉学科物理及相关领域的科学与技术 提交时间: 2016-05-08
摘要: 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.