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Biomotor is not a Heat Engine 生物电机不是热机
Pub Date : 2022-08-10 DOI: 10.1142/s1793048022310014
Yao-Gen Shu, Z. Ou-Yang
ATP synthase (FoF1-ATPase) is the model rotary molecular motor with three sites of ATP syntheses/hydrolyses in the “stator” of F1. The coupling between chemical progress and mechanical one is tight, and both progresses are reversible. Thus, the mechanochemical reversibility of FoF1-ATPase may resemble that of a heat engine. Single-molecule experiment has demonstrated that the efficiency of rotary motor is nearly 100%. However, it is impossible for a heat engine to achieve such high efficiency. On the other hand, kinesin is the model linear biomotor with only two sites of ATP hydrolyses located in the two heads, respectively, while its efficiency is just [Formula: see text]. Myosin V is another processive linear motor with nearly [Formula: see text] efficiency as well. However, the chemical progress of processive linear motors with two heads is irreversible. That is, if they walk backward in hand over hand along with a track by an external force, the energy molecule ATP is not synthesized, but consumed yet. This chemical irreversibility excludes the possibility that kinesin/myosin V can be treated energetically as a heat engine. The most intriguing fact is why the efficiency of a processive linear motor with two sites is just [Formula: see text] of that of a processive rotary motor with three sites.
ATP合成酶(FoF1-ATP酶)是一种模式旋转分子马达,在F1的“定子”中有三个ATP合成/水解位点。化学进展和机械进展之间的耦合是紧密的,并且两者都是可逆的。因此,FoF1-ATP酶的机械化学可逆性可能类似于热机。单分子实验表明,旋转电机的效率接近100%。然而,热力发动机不可能实现如此高的效率。另一方面,驱动蛋白是一种模型线性生物马达,只有两个ATP水解位点分别位于两个头中,而其效率仅为[公式:见正文]。Myosin V是另一种效率接近[公式:见正文]的加工线性电机。然而,双头加工线性电机的化学进步是不可逆转的。也就是说,如果他们在外力的作用下沿着轨道手挽手向后走,能量分子ATP不会合成,而是被消耗掉。这种化学不可逆性排除了驱动蛋白/肌球蛋白V可以作为热机进行能量处理的可能性。最有趣的事实是,为什么具有两个位置的加工线性电机的效率只是具有三个位置的处理旋转电机的效率的[公式:见正文]。
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引用次数: 0
Nonequilibrium Transport Induced by Biological Nanomachines 生物纳米机器诱导的非平衡输运
Pub Date : 2022-06-02 DOI: 10.1142/S1793048022310026
Yuto Hosaka, S. Komura
Biological nanomachines are nanometer-size macromolecular complexes that catalyze chemical reactions in the presence of substrate molecules. The catalytic functions carried out by such nanomachines in the cytoplasm, and biological membranes are essential for cellular metabolism and homeostasis. During catalytic reactions, enzymes undergo conformational changes induced by substrate binding and product release. In recent years, these conformational dynamics have been considered to account for the nonequilibrium transport phenomena such as diffusion enhancement, chemotaxis, and substantial change in rheological properties, which are observed in biological systems. In this paper, we shall give an overview of the recent theoretical and experimental investigations that deal with nonequilibrium transport phenomena induced by biological nanomachines such as enzymes or proteins.
生物纳米机器是纳米大小的大分子复合物,在底物分子存在的情况下催化化学反应。这些纳米机器在细胞质和生物膜中发挥的催化功能对细胞代谢和稳态至关重要。在催化反应中,酶通过底物结合和产物释放引起构象变化。近年来,这些构象动力学被认为可以解释生物系统中观察到的非平衡输运现象,如扩散增强、趋化性和流变性质的实质性变化。在本文中,我们将概述最近的理论和实验研究,这些研究处理由酶或蛋白质等生物纳米机器引起的非平衡转运现象。
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引用次数: 5
Investigation on Ultrasound Long Bone Fracture Imaging using the Migration Method 长骨骨折超声显像迁移法的研究
Pub Date : 2022-04-07 DOI: 10.1142/s1793048022500023
Ruth Kanyana, A. O. Olaniyan, Afam Uzorka
Ultrasound imaging plays a critical role in diagnostics in biomedicine because of its safety, nature, and low cost. Conventional ultrasound systems form images using a focused beam during transmission and dynamic focusing during the reception. The area under examination can be simultaneously insonified using a plane wave, which allows for ultrafast data capture rates but lowers image quality. The resultant image can be improved by coherent plane-wave compounding, in which numerous plane waves are released at different angles to produce distinct image datasets that are then blended to improve the final composite image. This study used the Fourier-domain technique for coherent plane-wave compounding image reconstruction from the image produced by conventional ultrasound to investigate the quality of the image produced compared to the X-ray image. To establish the merits and limitations of this approach, the researchers provided quantitative comparisons with the images obtained by the X-ray machine. The evaluation results are based on the peak signal-to-noise ratio (PSNR), mean, and variance. The results obtained showed that the migration method can precisely image the cortical bone fracture and offer good contrast between the bone tissue and the subcutaneous tissues.
超声成像以其安全、自然、低成本等优点在生物医学诊断中发挥着重要作用。传统的超声系统在传输过程中使用聚焦光束形成图像,在接收过程中使用动态聚焦。检查区域可以同时使用平面波进行非相干化,这可以实现超快的数据捕获速率,但会降低图像质量。所得到的图像可以通过相干平面波合成得到改善,在相干平面波合成中,许多平面波以不同的角度释放,产生不同的图像数据集,然后混合以改善最终的合成图像。本研究使用傅里叶域技术对常规超声图像进行相干平面波复合图像重建,以研究与x射线图像相比产生的图像质量。为了确定这种方法的优点和局限性,研究人员提供了与x射线机获得的图像的定量比较。评估结果基于峰值信噪比(PSNR)、均值和方差。结果表明,该方法能精确成像皮质骨骨折,并能提供良好的骨组织和皮下组织对比。
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引用次数: 0
Dynamical System Analysis of a Mathematical Model of Mild Atherosclerosis 轻度动脉粥样硬化数学模型的动力学系统分析
Pub Date : 2022-04-07 DOI: 10.1142/s1793048022500011
D. Mukherjee
Atherosclerosis, a long-term inflammatory affliction, occurs due to plaque accumulation in the intima, the innermost layer of artery. It is one of the prime causes of deaths from several cardio-vascular diseases. The primary interaction between oxidized low density lipoprotein (LDL) and macrophages in forming fatty steak is presented here in terms of a nonlinear reaction-diffusion system in one spatial dimension under Neumann boundary conditions. Both the spatio-temporal and the temporal models are analyzed qualitatively. Numerical simulations of both the model systems lead to three significant model parameters with respect to which bifurcations are found. Bifurcating parameters indicate possible developments of various therapeutic strategies in order to establish any preventative measures for an individual or group of patients. It has been found that ingestion rate of oxidized LDL by macrophages has a great impact on the plaque forming process.
动脉粥样硬化是一种长期的炎症性疾病,是由于动脉内膜(最内层)的斑块堆积引起的。它是导致多种心血管疾病死亡的主要原因之一。在Neumann边界条件下,氧化低密度脂蛋白(LDL)和巨噬细胞在形成脂肪牛排过程中的主要相互作用是在一维非线性反应扩散系统中提出的。对时空模型和时间模型进行了定性分析。对这两个模型系统的数值模拟得出了三个重要的模型参数,关于这些参数可以发现分叉。分叉参数表明各种治疗策略的可能发展,以便为个体或患者组制定任何预防措施。研究发现,巨噬细胞摄入氧化低密度脂蛋白的速率对斑块的形成过程有很大影响。
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引用次数: 1
Author Index Volume 16 (2021) 作者索引第16卷(2021年)
Pub Date : 2021-12-01 DOI: 10.1142/s1793048021990010
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引用次数: 0
Conductivity Mechanism of Ion–DNA Interaction in Dilute Solution 离子- dna在稀溶液中相互作用的传导机理
Pub Date : 2021-09-11 DOI: 10.1142/s1793048021500077
Lingyun Zhang
In this paper, we propose an impurity scattering model of quasi-one-dimensional disordered system for ion–DNA interaction in dilute solution based on the density of state in non-periodic DNA. This disordered system is composed of cations and DNA, the hydrogen ions adsorbed on the surface of DNA with negative charges are considered as impurities. It is hydrogen ions in hydration layer that cause the variations of the density of state near the Fermi level. The classical theory describes the linear dependence of conductivity on concentration. By developing the Green function approach of ion–DNA interaction in the dilute solution, the quantum theory not only gives the linear part but also demonstrates the nonlinear part of the conductivity.
本文基于非周期DNA的态密度,提出了稀溶液中离子- DNA相互作用准一维无序系统的杂质散射模型。该无序体系由阳离子和DNA组成,吸附在DNA表面带负电荷的氢离子被认为是杂质。水合层中的氢离子引起了费米能级附近态密度的变化。经典理论描述了电导率与浓度的线性关系。通过发展离子- dna在稀溶液中相互作用的格林函数方法,量子理论不仅给出了电导率的线性部分,而且证明了电导率的非线性部分。
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引用次数: 0
Figure-of-Merit for a Long-Term Survivorship of a Species Determined from the Short-Term Mortality Rate of Its Individual Organisms 根据单个生物的短期死亡率确定一个物种长期存活的优点图
Pub Date : 2021-09-01 DOI: 10.1142/s1793048021500065
E. Suhir
The two analytical (“mathematical”) probabilistic predictive models considered in this analysis suggest that (1) the nonrandom time-derivative of the long-term mortality rate at a rather arbitrary initial moment of time for a particular type of species of interest can be viewed as a suitable physical or biological criterion, a sort of a figure of merit (FoM), of its long-term viability/survivorship and that (2) this derivative can be determined as the variance of the random mortality rate for the significantly shorter, of course, lifespan of the individual organisms that the type of species as a whole, addressed by the first model, is comprised of. This suggestion is obtained as a modification and extension of and as an “analogy” to a concept that the author developed earlier in application to microelectronics products. So, it is assumed in our approach that the long-term survivorship of a species comprised of numerous individual organisms is analogous to the long-term performance of an electronic product comprised of numerous mass-produced components. In the original research, it was shown that the time-derivative at the initial moment of time of the nonrandom infant mortality portion (IMP) of the bathtub curve (BTC) for an electronic product is, in effect, the variance of the random failure rate (RFR) of the mass-produced components that this product is comprised of, and it is assumed that such an analogy is applicable also to the long-term survivorship of a species comprised of numerous individual organisms. The larger this variance, the shorter is the expected long-term lifetime (survivorship) of the species as a whole. Future work should be focused, first of all, on the verification of the trustworthiness of our basic assumption for different species, including humans, and on the accumulation of statistical data for long-term survivorship of various species and their existing or future habitats, with consideration of the roles of gravity, temperature, level of radiation, attributes of the atmosphere, if any, etc., as well as on calculating lifespan variances for the organisms that the species of interest are comprised of.
本分析中考虑的两个分析(“数学”)概率预测模型表明:(1)特定类型感兴趣物种在相当任意的初始时刻的长期死亡率的非随机时间导数可以被视为一种合适的物理或生物学标准,一种优值(FoM),其长期生存能力/存活率,以及(2)该衍生物可以被确定为由第一个模型处理的物种类型作为一个整体所组成的个体生物的寿命明显较短的随机死亡率的方差。这一建议是对作者早期在微电子产品应用中提出的一个概念的修改和扩展,也是对该概念的“类比”。因此,在我们的方法中,假设由许多个体生物组成的物种的长期生存能力类似于由大量生产的组件组成的电子产品的长期性能。在最初的研究中,研究表明,电子产品浴缸曲线(BTC)的非随机婴儿死亡率部分(IMP)在初始时刻的时间导数实际上是该产品所包含的大量生产部件的随机故障率(RFR)的方差,并且假设这样的类比也适用于由许多个体生物组成的物种的长期生存。这个方差越大,整个物种的预期长期寿命(生存期)就越短。未来的工作首先应侧重于验证我们对包括人类在内的不同物种的基本假设的可信度,并积累各种物种及其现有或未来栖息地的长期生存统计数据,同时考虑到重力、温度、辐射水平、大气属性(如有),以及计算感兴趣物种所包含的生物体的寿命方差。
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引用次数: 1
Supramolecular Chemistry of Folic Acid — Experimental and Computational Investigation 叶酸的超分子化学——实验与计算研究
Pub Date : 2021-08-11 DOI: 10.1142/s1793048021500053
Pravalika Butreddy, Selina Laws, Premitha Pansalawatte, E. Laws, H. Rathnayake
Supramolecular chemistry of folic acid is studied and revealed by exploring its assembly and disassembly process in a liquid–liquid interface. Experimental and computational studies are conducted to understand the interfacial interactions of folic acid in a oil-in-water interface by investigating the role of folic acid’s critical aggregation concentration (CAC), molecular arrangement, and intermolecular interactions at the molecular level. The folic acid’s CAC, determined from the concentration-dependent UV–vis absorption spectra in water/methanol solvent system, is found to be 2.72[Formula: see text][Formula: see text]M. The sigmoidal behavior of folic acid’s maximum absorbances with respect to different folic acid concentrations reveals the nature of the self-assembly dynamics and aggregative assemblies’ formation by three signature phases, in which CAC lies in the second phase — the growth phase. The computational studies reveal the intermolecular interactions and molecular orientation of folic acid molecules. They interact each other via H2-bonding between carboxylic acid groups in two glutamate units and two amine groups in pteridine units and [Formula: see text]–[Formula: see text] interactions between pteridine units and phenyl units, orienting two units in a parallel stacked arrangement. Correlating the computed intermolecular interactions and structural orientation of folic acid with its solid-state crystal packing structure has provided strong evidence supporting its supramolecular chemistry and assembly dynamics to make nanoassemblies in a liquid–liquid interface.
通过探索叶酸在液-液界面中的组装和拆卸过程,研究并揭示了叶酸的超分子化学。通过研究叶酸的临界聚集浓度(CAC)、分子排列和分子水平上的分子间相互作用,进行了实验和计算研究,以了解叶酸在水包油界面中的界面相互作用。根据水/甲醇溶剂体系中的浓度依赖性紫外-可见吸收光谱测定,叶酸的CAC为2.72[公式:见正文][公式:见文本]M。叶酸最大吸收率相对于不同叶酸浓度的s型行为揭示了自组装动力学的性质和由三个特征阶段形成的聚集组装体,其中CAC处于第二阶段——生长阶段。计算研究揭示了叶酸分子的分子间相互作用和分子取向。它们通过两个谷氨酸单元中的羧酸基团和蝶呤单元中的两个胺基团之间的H2键相互作用,以及蝶呤单元和苯基单元之间的[式:见正文]–[式:参见正文]相互作用,将两个单元定向为平行堆叠排列。将叶酸的分子间相互作用和结构取向与其固态晶体填充结构相关联,为其在液-液界面中制造纳米组装体的超分子化学和组装动力学提供了有力的证据。
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引用次数: 0
On the Search for Brain Bifurcation Parameters: Lessons From FMRI Studies on Visual Illusions 脑分叉参数的搜索——FMRI视觉错觉研究的启示
Pub Date : 2021-08-05 DOI: 10.1142/s1793048021500041
T. Frank, P. Stowik
Data from three functional magnetic resonance imaging (fMRI) studies that involved in total about 100 participants and showed that the strength of several visual illusions such as the Ebbinghaus, Ponzo, and Muller-Lyer illusions depends on neuroanatomical subject measures such as visual cortex surface area and parahippocampal cortex gray matter volume were evaluated using a dynamical systems perspective to determine brain bifurcation parameters. Bifurcation parameters that involved power laws and captured relational dependencies were fitted separately to the three fMRI studies. The bifurcation parameter hypothesis that states that such parameters show unique quantities and are no longer correlated to structural systems properties was tested. The power law exponents and mean bifurcation parameter values were determined. For all three studies and three illusion types, the bifurcation parameter hypothesis was supported. Accordingly, the constructed parameters characterized the reactions of the participants under the Ebbinghaus, Ponzo, and Muller-Lyer illusions in terms of unique threshold values that no longer depended on neuroanatomical subject measures. Power law exponents in the range from 1 to 7 were found. The fMRI data describing gray matter volume of certain active regions in the parahippocampal cortex showed some interesting relationship between the mean bifurcation parameter values.
来自三项功能性磁共振成像(fMRI)研究的数据共涉及约100名参与者,Muller-Lyer错觉取决于神经解剖学受试者的测量,如视觉皮层表面积和海马旁皮层灰质体积。涉及幂律和捕获的关系依赖性的分叉参数分别拟合到三项fMRI研究中。分叉参数假说表明,这些参数显示出独特的数量,并且不再与结构系统特性相关。确定了幂律指数和平均分岔参数值。对于所有三项研究和三种错觉类型,分叉参数假说得到了支持。因此,所构建的参数根据不再依赖于神经解剖学受试者测量的独特阈值来表征参与者在Ebbinghaus、Ponzo和Muller-Lyer错觉下的反应。幂律指数在1到7之间。描述海马旁皮层某些活动区域灰质体积的fMRI数据显示,平均分叉参数值之间存在一些有趣的关系。
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引用次数: 0
The Possibility of Quantum Medicine in Cancer Research: A Review 量子医学在癌症研究中的可能性综述
Pub Date : 2021-06-07 DOI: 10.1142/S1793048021300012
M. Faramarzpour, Mohammadreza Ghaderinia, Hamed Abadijoo, H. Aghababa
There is no doubt that quantum mechanics has become one of the building blocks of our physical world today. It is one of the most rapidly growing fields of science that can potentially change every aspect of our life. Quantum biology is one of the most essential parts of this era which can be considered as a game-changer in medicine especially in the field of cancer. Despite quantum biology having gained more attention during the last decades, there are still so many unanswered questions concerning cancer biology and so many unpaved roads in this regard. This review paper is an effort to answer the question of how biological phenomena such as cancer can be described through the quantum mechanical framework. In other words, is there a correlation between cancer biology and quantum mechanics, and how? This literature review paper reports on the recently published researches based on the principles of quantum physics with focus on cancer biology and metabolism.
毫无疑问,量子力学已经成为我们今天物理世界的基石之一。它是发展最快的科学领域之一,有可能改变我们生活的方方面面。量子生物学是这个时代最重要的部分之一,它可以被认为是医学领域的游戏规则改变者,特别是在癌症领域。尽管量子生物学在过去的几十年里获得了更多的关注,但关于癌症生物学仍然有很多未解之谜,在这方面还有很多未铺设的道路。这篇综述文章是为了回答如何通过量子力学框架来描述癌症等生物现象的问题。换句话说,癌症生物学和量子力学之间是否存在关联,以及如何关联?本文综述了近年来基于量子物理原理的研究成果,重点介绍了肿瘤生物学和代谢方面的研究进展。
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引用次数: 0
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Biophysical reviews and letters
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