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Quantum States in Templated Biological Processes 模板化生物过程中的量子态
Pub Date : 2021-05-26 DOI: 10.4236/ojbiphy.2021.113009
R. Englman
Living matter is characterized by its variegated potential energy landscape possessing a proneness to continually absorb externally supplied energy. This enables it to ascend from its momentary energy minimum state to one of its myriad barriers only to subsequently descend to a new minimum with a potentiality to perform new functions or processes, in the while exuding energy (mainly in the form of heat). As in studies of molecular intersystem crossing, the jumping processes are describable in terms of quantum states. In this work we derive the low energy quantum states for those three templated self-assembling processes, self-replication, metabolism and self-repair that are commonly regarded as distinguishing animate from inanimate substance. The outcome of each process is a new, long-living, stable molecular aggregate characterized by its specific conformation, comprising a host of micro-states associated with sub-conformations and patterned upon the template. The provenance of these newly-formed states is obtained here by a unified formalism for all three processes, based on a Hamiltonian, constructed in an abstract Hilbert-space framework, whose essences are bilinear coupling terms in the Hamiltonian between the template and the bath, as well as between the reactants and the bath. Treating these terms by second order perturbation, one finds in low lying quantum states an alignment between the template and the product, somewhat analogous to the Kramers-Anderson superexchange mechanism, with the bath replacing the bridging anion and by exploitation of the decohering due to the randomness of the bath. The idea underlying this work, recurrent in the biological literature and here expressed in a Physics, Hamiltonian framework, is the correlative unity of the whole biological system comprising multiple organs.
有生命的物质具有不断吸收外界供给的能量的倾向,其特点是势能格局的多样性。这使它能够从瞬时能量最小状态上升到无数障碍之一,然后下降到具有执行新功能或过程的新最小值,同时释放能量(主要以热的形式)。在分子系统间交叉的研究中,跳跃过程可以用量子态来描述。在这项工作中,我们推导了三种模板自组装过程的低能量量子态,自我复制,代谢和自我修复通常被认为是区分有生命和无生命的物质。每个过程的结果都是一个新的、长寿命的、稳定的分子聚集体,其特征是其特定的构象,包括与亚构象相关的许多微观状态,并在模板上形成图案。这些新形成的状态的来源是通过统一的三个过程的形式得到的,基于一个抽象的希尔伯特空间框架中构造的哈密顿量,其本质是模板和槽之间以及反应物和槽之间的哈密顿量中的双线性耦合项。通过二阶扰动处理这些项,人们发现在低洼量子态中模板和产物之间有一种排列,有点类似于Kramers-Anderson超交换机制,其中槽取代了桥接阴离子,并利用了由于槽的随机性而产生的退相干。这项工作背后的思想,在生物学文献中反复出现,在这里用物理学的哈密顿框架来表达,是由多个器官组成的整个生物系统的相关统一性。
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引用次数: 0
Evaluation of Peppermint Leaf Flavonoids as SARS-CoV-2 Spike Receptor-Binding Domain Attachment Inhibitors to the Human ACE2 Receptor: A Molecular Docking Study 薄荷叶总黄酮作为SARS-CoV-2刺突受体结合域对人ACE2受体的附着抑制剂的评价:分子对接研究
Pub Date : 2021-02-25 DOI: 10.4236/ojbiphy.2022.122005
M. Júnior, Rafael Timóteo de Sousa Júnior, G. A. Nze, W. Giozza, L. A. R. Júnior
Virtual screening is a computational technique widely used for identifying small molecules which are most likely to bind to a protein target. Here, we performed a molecular docking study to propose potential candidates to prevent the RBD/ACE2 attachment. These candidates are sixteen different flavonoids present in the peppermint leaf. Results showed that Luteolin 7-O-neohesperidoside is the peppermint flavonoid with a higher binding affinity regarding the RBD/ACE2 complex (about -9.18 Kcal/mol). On the other hand, Sakuranetin presented the lowest affinity (about -6.38 Kcal/mol). Binding affinities of the other peppermint flavonoids ranged from -6.44 Kcal/mol up to -9.05 Kcal/mol. The binding site surface analysis showed pocket-like regions on the RBD/ACE2 complex that yield several interactions (mostly hydrogen bonds) between the flavonoid and the amino acid residues of the proteins. This study can open channels for the understanding of the roles of flavonoids against COVID-19 infection.
虚拟筛选是一种广泛用于识别最有可能与蛋白质靶标结合的小分子的计算技术。在这里,我们进行了一项分子对接研究,以提出防止RBD/ACE2附着的潜在候选者。这些候选者是存在于薄荷叶中的十六种不同的黄酮类化合物。结果表明,木犀草素7-O-新橙皮苷是对RBD/ACE2复合物具有较高结合亲和力(约-9.18Kcal/mol)的薄荷类黄酮。另一方面,Sakuranetin表现出最低的亲和力(约-6.38kcal/mol)。其他薄荷类黄酮的结合亲和力范围从-6.44千卡/摩尔到-9.05千卡/mol。结合位点表面分析显示,RBD/ACE2复合物上的口袋状区域在类黄酮和蛋白质的氨基酸残基之间产生了几种相互作用(主要是氢键)。这项研究可以为了解黄酮类化合物对新冠肺炎感染的作用开辟渠道。
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引用次数: 4
Internal Electrical Noises of BioFET Sensors Based on Various Architectures 基于不同结构的生物晶体管传感器内部电噪声
Pub Date : 2021-02-07 DOI: 10.4236/OJBIPHY.2021.112006
L. Gasparyan, F. Gasparyan, V. Simonyan
The results of a comparative literature analysis of internal electrical noises and signal-to-noise ratio for nanoscale BioFET (biological field-effect transistor) and DNA (deoxyribonucleic acid) sensors based on different architectures MIS (metal-insulator-semiconductor), EIS (electrolyte-insulator-semi-conductor) and ISFET (ion-selective field-effect transistor) are presented. Main types, models and mechanisms of internal noises of bio- & chemical field-effect based sensors are analyzed, summarized and presented. For the first time, corresponding detail electrical equivalent circuits were built to calculate the spectral densities of noises generated in the active part of a solid (semiconductor, dielectric) and in an aqueous solution for MIS, EIS and ISFET structures based sensors. Complete expressions are obtained for the rms (root mean square) value of the noise current (or voltage), as well as the noise spectral densities for the architectures under study. The miniaturization of biosensors leads to a decrease in the level of the useful signal-current. For successful operation of the sensor, it is necessary to ensure a high value of the SNR (signal-to-noise ratio). In case of weak useful signals, it is necessary to reduce the level of internal electrical noise. This work is devoted to a detailed study of the types and mechanisms of internal electrical noises in specific biosensor architectures.
介绍了基于不同结构MIS(金属绝缘体半导体)、EIS(电解质绝缘体半导体)和ISFET(离子选择场效应晶体管)的纳米级生物场效应晶体管和DNA(脱氧核糖核酸)传感器的内部电噪声和信噪比的对比文献分析结果。分析、总结和介绍了基于生化场效应的传感器内部噪声的主要类型、模型和机理。首次建立了相应的详细等效电路,以计算基于MIS、EIS和ISFET结构的传感器在固体(半导体、电介质)的活性部分和水溶液中产生的噪声的频谱密度。获得了噪声电流(或电压)的均方根值以及所研究架构的噪声频谱密度的完整表达式。生物传感器的小型化导致有用信号电流水平的降低。为了传感器的成功操作,有必要确保SNR(信噪比)的高值。在有用信号较弱的情况下,有必要降低内部电噪声的水平。这项工作致力于详细研究特定生物传感器结构中内部电噪声的类型和机制。
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引用次数: 1
A Quantum State Scenario for Biological Self-Replication 生物自我复制的量子态场景
Pub Date : 2021-02-07 DOI: 10.4236/OJBIPHY.2021.112005
R. Englman
With the prevalent conception of self-replication (SR, a hallmark of living systems) as a non-equilibrium process subject to thermodynamic laws, a complementary approach derives the low energy quantum states arising from a Hamiltonian that appears to be specific for bio-systems by its containing some strongly binding terms. The bindings attract properties of the template (T) and the reactants to form a replicate (R). The criterion for SR that emerges from the theory is that second order (bi-linear) interaction terms between degrees of motion of T-R and the thermal bath dominate negatively over a linear self-energy term, and thereby provide a binding between the attributes of T and R. The formalism (reminiscent of the Kramers-Anderson mechanism for superexchange) is from first principles, but hinges on a drastic simplification by modelling the T, R and bath variables on interacting qubits and by congesting the attraction into a single (control) parameter. The development relies on further simplifying features, such as Random Phase Approximations and an Effective Hamiltonian formalism. The entropic balance to replication is considered and found to reside in the far surroundings.
由于自复制(SR,生命系统的标志)是一个受热力学定律约束的非平衡过程的普遍概念,一种互补的方法推导出了由哈密顿量产生的低能量子态,该哈密顿量似乎是生物系统特有的,因为它包含一些强结合项。结合吸引模板(T)和反应物的性质以形成复制物(R)。从该理论中得出的SR的标准是,T-R和热浴的运动度之间的二阶(双线性)相互作用项负支配线性自能项,从而在T和R的属性之间提供了绑定。形式主义(让人想起超交换的Kramers-Anderson机制)来自第一原理,但这取决于通过在相互作用的量子位上建模T、R和bath变量以及通过将吸引力凝聚成单个(控制)参数来进行大幅简化。该发展依赖于进一步简化的特征,如随机相位近似和有效哈密顿形式。复制的熵平衡被认为存在于遥远的环境中。
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引用次数: 1
The Spreading Depression Propagation: How Electrochemical Patterns Distort or Create Perception 扩散抑制传播:电化学模式如何扭曲或创造感知
Pub Date : 2021-02-07 DOI: 10.4236/OJBIPHY.2021.112003
V. M. F. Lima, Alfredo Pereira Junior, Guilherme Lima de Oliveira
At the transition from quiescence to propagating waves recorded in isolated retinas, a circular electric current closes in the extracellular matrix; this circular current creates a magnetic torus flow that, when entering quiescent tissue in front of the wave, recruits elements and when leaving behind, helps to build the absolute refractory state. The waving magnetic torus is the consequence of the vortex effect and explains the energy boost that drives propagation. Methods: We interpret experimental results from intrinsic and extrinsic fluorescence dyes, voltage, calcium and pH sensitive, optical signals from isolated retinas, and time series recordings using ion exchange resins: Ca, K, pH, Na, Cl recorded extracellularly at retinas, cerebellums and cortices coupled to spreading depression waves. Finally, we checked the ECoG activity, also a time series, at the transition from after discharges to spreading depression in rat hippocampus. Results: The integrated assessment of the diversified measurements led to the realization that the magnetic flow at the wavefront is a major contributor to the wave propagation mechanisms. This flow couples mass and charge flows as a swirling torus from excited to quiescent tissue. Conclusions: An alternative model of the brain is possible, apart from the classical HH and molecular biology model. Physical chemistry of charged gels and its flows explains the results. The conceptual framework uses far from equilibrium thermodynamics.
在离体视网膜中记录到的从静止到传播波的转变中,一个圆形电流在细胞外基质中闭合;这种圆形电流产生磁环流,当进入波前的静止组织时,吸收元素,当离开时,有助于建立绝对难熔状态。波动磁环是涡旋效应的结果,并解释了驱动传播的能量提升。方法:我们对实验结果进行了解释,这些实验结果来自于内源性和外源性荧光染料,电压,钙和pH敏感,来自分离视网膜的光信号,以及使用离子交换树脂的时间序列记录:Ca, K, pH, Na, Cl在视网膜,小脑和皮层的细胞外记录,与传播的抑郁波耦合。最后,我们检查了大鼠海马从放电后到扩散性抑郁过渡时期的ECoG活动,也是一个时间序列。结果:综合评价各种测量结果,认识到波前磁流是波传播机制的主要贡献者。这种流动耦合了质量和电荷的流动,形成一个从激发态组织到静止组织的旋转环。结论:除了经典的HH和分子生物学模型外,可能还有另一种大脑模型。带电凝胶及其流动的物理化学解释了这一结果。其概念框架采用了远离平衡态的热力学。
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引用次数: 2
Survival at Tumor Recurrence in Soft Matter 软质肿瘤复发时的生存率
Pub Date : 2021-02-07 DOI: 10.4236/OJBIPHY.2021.112004
I. Trifonova, G. Kurteva, S. Z. Stefanov
Survival at tumor recurrence in soft matter, after chemotherapy, is assessed by RNA folding. It is shown that this recurrence is starting with development of a fluidlike globule; it changes the energy of soft matter; it proceeds as a resonant mixing; and at the end it causes diffusion. This diffusion is interpreted as metastasis in soft matter. A tumor memory is designed for its recurrence oscillations. These oscillations are marked as positive or negative according to their influence on life stabilization or destabilization. It is demonstrated that a tumor memorizes two types of recurrences. The intensity of chemotherapy in soft matter for a tumor with such memory is obtained. Survival at tumor recurrence in soft matter, after chemotherapy, is assigned to one of the five regions of the phase diagram of the “thermalized” tumor by microenvironment. To each of these regions is collated a breast cancer survival class. It is found that the survival at tumor recurrence in soft matter, after chemotherapy, well represents actual survival of 32 patients with breast cancer.
化疗后软质肿瘤复发的存活率通过RNA折叠进行评估。研究表明,这种复发始于流体样球的发展;它改变了软物质的能量;它作为共振混合进行;并且在最后它引起扩散。这种扩散被解释为软质转移。肿瘤记忆是为其复发振荡而设计的。根据这些振荡对生命稳定或不稳定的影响,将其标记为正振荡或负振荡。研究表明,肿瘤会记忆两种类型的复发。获得了具有这种记忆的肿瘤在软质中的化疗强度。化疗后软质肿瘤复发时的存活率被微环境分配到“热化”肿瘤相图的五个区域之一。这些区域中的每一个区域都有一个癌症生存分类。研究发现,软质肿瘤复发时,化疗后的生存率很好地代表了32例癌症患者的实际生存率。
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引用次数: 0
Approaching Complexity: Hyperthermia Dose and Its Possible Measurement in Oncology 接近复杂性:肿瘤学中的热疗剂量及其可能的测量
Pub Date : 2021-01-27 DOI: 10.4236/OJBIPHY.2021.111002
O. Szász, A. Szász
A heuristic stochastic solution of the Pennes equation is developed in this paper by applying the self-organizing, self-similar behaviour of living structures. The stochastic solution has a probability distribution that fits well with the dynamic changes in the living objects concerned and eliminates the problem of the deterministic behaviour of the Pennes approach. The solution employs the Weibull two-parametric distribution which offers satisfactory delivery of the rate of temperature change by time. Applying the method to malignant tumours obtains certain benefits, increasing the efficacy of the distortion of the cancerous cells and avoiding doing harm to the healthy cells. Due to the robust heterogeneity of these living systems, we used thermal and bioelectromagnetic effects to distinguish the malignant defects, selecting them from the healthy cells. On a selective basis, we propose an optimal protocol using the provided energy optimally such that molecular changes destroy the malignant cells without a noticeable effect on their healthy counterparts.
本文利用生物结构的自组织、自相似行为,给出了Pennes方程的一个启发式随机解。随机解的概率分布能很好地适应有关生物对象的动态变化,并消除了Pennes方法的确定性行为问题。该方案采用威布尔双参数分布,提供了令人满意的温度随时间变化的速率。将该方法应用于恶性肿瘤,既增加了对癌细胞的扭曲作用,又避免了对健康细胞的伤害,取得了一定的效益。由于这些生命系统的强大异质性,我们使用热效应和生物电磁效应来区分恶性缺陷,从健康细胞中选择它们。在选择性的基础上,我们提出了一个最佳的方案,利用提供的能量,使分子变化破坏恶性细胞,而不会对其健康对应的显著影响。
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引用次数: 7
ROC and SAT Analysis of Different Grayscale Test Images (Distractors L and Target T) to Customize a Visual-Search Attention Task 不同灰度测试图像(干扰物L和目标T)定制视觉搜索注意任务的ROC和SAT分析
Pub Date : 2021-01-01 DOI: 10.4236/ojbiphy.2021.114017
D. Chuckravanen, Barkin Ilhan, N. Dalkilic
Nowadays, there is a great need to investigate the effects of fatigue on physical as well as mental performance. The issues that are generally associated with extreme fatigue are that one can easily lose one’s focus while performing any particular activity whether it is physical or mental and this decreases one’s motivation to complete the task at hand efficiently and successfully. In the same line of thought, myriads of research studies posited the negative effects of fatigue on mental performance, and most techniques to induce fatigue to require normally long-time and repetitive visual search tasks. In this study, a visual search algorithm task was devised and customized using performance measures such as d’ (d-prime) and Speed Accuracy Trade-Off (SATF) as well as ROC analysis for classifier performance. The visual search algorithm consisted of distractors (L) and a target (T) whereby human participants had to press the appropriate keyboard button as fast as possible if they notice a target or not upon presentation of a visual stimulus. It was administered to human participants under laboratory conditions, and the reaction times, as well as accuracy of the participants, were monitored. It was found that the test image Size35Int255 was the best image to be used in terms of sensitivity and AUC (Area under Curve). Therefore, ongoing researches can use these findings to create their visual stimuli in such a way that the target and distractor images follow the size and intensity characteristics as found in this research.
现在,很有必要研究疲劳对身体和精神表现的影响。通常与极度疲劳相关的问题是,一个人在进行任何特定的活动时,无论是身体上的还是精神上的,都很容易失去注意力,这降低了一个人高效、成功地完成手头任务的动力。在同样的思路下,无数的研究假设了疲劳对智力表现的负面影响,并且大多数诱导疲劳的技术通常需要长时间和重复的视觉搜索任务。在本研究中,使用d ' (d-prime)和速度精度权衡(SATF)等性能指标以及分类器性能的ROC分析,设计并定制了视觉搜索算法任务。视觉搜索算法由干扰物(L)和目标(T)组成,人类参与者必须尽可能快地按下适当的键盘按钮,如果他们在视觉刺激出现时注意到目标或没有注意到目标。在实验室条件下,它被施用于人类参与者,并监测反应时间,以及参与者的准确性。在灵敏度和曲线下面积(AUC)方面,我们发现测试图像Size35Int255是最好的图像。因此,正在进行的研究可以利用这些发现来创造他们的视觉刺激,使目标和干扰图像遵循本研究中发现的大小和强度特征。
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引用次数: 0
Inventory of Radiation Protection in Hospitals of Level III in Senegal 塞内加尔三级医院辐射防护清单
Pub Date : 2021-01-01 DOI: 10.4236/ojbiphy.2021.114016
B. Ndong, Sidi Ahmed Dia, M. S. Djigo, H. Fachinan, E. Bathily, O. Diop, K. Ka, G. Akpo, El Hadji Fallou Diouf, L. Diouf, Pape Mady Sy, A. Djiboune, G. Mbaye, Magu Diagne, Omar Ndoye, M. Mbodji
The aim of this study was to evaluate the level of protection of employees who are exposed to radiation in a level III hospital establishment. It was a descriptive cross-sectional survey of six months’ duration, involving eight level III Hospitals (Aristide Le Dantec, Fann, Hoggy, Hear, Abass Ndao, Pikine, Touba, and Thiès) in Senegal. Sixty-one of the one hundred questionnaires were recovered (overall response rate of 61%). The population of the study was mainly female (54.1%). The average age was 38.57 with extremes ranging from 23 to 65 years old. In the places where ionizing radiation sources are handled, only at the Aristide Le Dantec Hospital did we find a “competent person in radiation protection”. This explained the lack of a classification of employees and work areas. Forty out of sixty-one (73.77%) had no knowledge of the basic principles of radiation protection (justification, optimisation, dose limitation) and had not ever taken radiation holidays. For radiovigilance, exposure time limits to ionizing radiation concerned only 29/61 or 47.54% of the study population. The inverse square law of distance was known by only 40 workers, of whom 15 had no compliance. We found the presence of dosifilms in only 7/61 or 11.47% of the workers. On the other hand, the use of lead aprons was well established and concerned 57/61 workers, i.e., 93.44%. In sum, ionizing radiation causes adverse health effects. The absence of a good radiation protection culture in Senegal requires the presence of at least 4 to 5 competent persons in radiation protection for quality training of workers in radiobiHow to cite this paper: Ndong, B., Dia, S.A., Djigo, M.S., Fachinan, H., Bathily, E.H.L., Diop, O., Ka, K., Akpo, G.L.K., Diouf, E.H.F., Diouf, L.A.D., Sy, P.M., Djiboune, A., Mbaye, G., Diagne, M., Ndoye, O. and Mbodji, M. (2021) Inventory of Radiation Protection in Hospitals of Level III in Senegal. Open Journal of Biophysics, 11, 397406. https://doi.org/10.4236/ojbiphy.2021.114016 Received: September 4, 2021 Accepted: October 26, 2021 Published: October 29, 2021 Copyright © 2021 by author(s) and Scientific Research Publishing Inc. This work is licensed under the Creative Commons Attribution International License (CC BY 4.0). http://creativecommons.org/licenses/by/4.0/ Open Access
本研究的目的是评估三级医院机构中受辐射照射的雇员的防护水平。这是一项为期6个月的描述性横断面调查,涉及塞内加尔的8家三级医院(Aristide Le Dantec、Fann、Hoggy、Hear、Abass Ndao、Pikine、Touba和thi)。100份问卷回收61份(总回复率61%)。研究人群以女性为主(54.1%)。平均年龄为38.57岁,极端年龄为23岁至65岁。在处理电离辐射源的地方,只有在阿里斯蒂德·勒丹特克医院,我们找到了一个"称职的辐射防护人员"。这解释了为什么没有对员工和工作区域进行分类。61人中有40人(73.77%)不了解辐射防护的基本原理(论证、优化、剂量限制),从未休过辐射假。在辐射警戒方面,电离辐射暴露时间限制仅涉及29/61或47.54%的研究人群。只有40名工人知道距离平方反比定律,其中15人没有遵守。我们发现只有7/61或11.47%的工人存在剂量膜。另一方面,铅围裙的使用得到了很好的确立,涉及57/61名工人,即93.44%。总之,电离辐射对健康造成不利影响。塞内加尔缺乏良好的辐射防护文化,要求至少有4到5名称职的辐射防护人员对放射性工作人员进行质量培训。如何引用本文:Ndong, B., Dia, S.A, Djigo, m.s., facchinan, H., Bathily, e.h.l., Diop, O., Ka, K., Akpo, g.l.k., Diouf, e.h.f., Diouf, L.A.D, Sy, pm, Djiboune, a ., Mbaye, G., Diagne, M., Ndoye, O.和Mbodji, M.(2021)塞内加尔三级医院辐射防护目录。生物物理学报,11,397406。https://doi.org/10.4236/ojbiphy.2021.114016收稿日期:2021年9月4日收稿日期:2021年10月26日出版日期:2021年10月29日版权所有©作者与科研出版公司。本作品采用知识共享署名国际许可协议(CC BY 4.0)。http://creativecommons.org/licenses/by/4.0/开放获取
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引用次数: 0
Novel Method Employing Accelerated-Oscillated Wave Saline Solutions to Unblock Blood Vessels—Physics and Fluid Dynamics Perspectives and Simulations 采用加速振荡波盐溶液疏通血管的新方法-物理和流体动力学的观点和模拟
Pub Date : 2021-01-01 DOI: 10.4236/ojbiphy.2021.114018
Stephon Stewart, D. Chuckravanen
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引用次数: 1
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生物物理学期刊(英文)
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