Calculi for interaction
咖啡酸激活酪氨酸酶催化反应的动力学研究
咖啡酸激活酪氨酸酶催化反应的动力学研究
邓湘庆;龚盛昭;张木全
【期刊名称】《食品科学》
【年(卷),期】2008(029)004
【摘要】在30℃,pH6.8的Na2HPO4-NaH2PO4缓冲体系中,采用酶动力学方法研究了咖啡酸对酪氨酸酶单酚酶和二酚酶活力的激活效应.实验结果表明,咖啡酸对酪氨酸酶单酚酶和二酚酶活性均有激活作用,对单酚酶和二酚酶活力的相对激活率达到50%的咖啡酸浓度(IC50)分别为0.27mmol/L和1.35mmol/L.咖啡酸能消除单酚酶催化反应的迟滞时间,对二酚酶的激活作用表现为混合性激活,当咖啡酸浓度为0、0.50、1.0、1.50mmol/L时,米氏常数Km分别为0.31、0.25、0.20、0.15mmol/L.
【总页数】4页(P98-101)
【作者】邓湘庆;龚盛昭;张木全
【作者单位】广东食品药品职业学院,广东广州,510520;广东轻工职业技术学院,广东广州,510300;广东轻工职业技术学院,广东广州,510300
【正文语种】中文
【中图分类】Q556.3
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1.肉桂酸抑制酪氨酸酶催化反应的动力学研究 [J], 龚盛昭;杨卓如;程江
2.肉桂酸甲酯抑制酪氨酸酶催化反应的动力学研究 [J], 龚盛昭;王晓立;林取妹;高
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5.土豆中酪氨酸酶的提取及植物精油对其激活作用与动力学研究 [J], 陈怀庆; 廖兴宏; 赵慧; 杨俊棋; 王文君; 张岩
因版权原因,仅展示原文概要,查看原文内容请购买。
蛋白质-适配体相互作用预测的方法
蛋白质-适配体相互作用预测的方法蛋白质-适配体相互作用是指蛋白质与其相互作用的小分子,如药物,抑制剂或配体之间的相互作用。
这种相互作用对于药物设计、酶动力学研究和疾病治疗非常重要。
预测和分析蛋白质-适配体相互作用的方法成为了当今生物医学研究领域的一个重要课题。
目前,有许多计算生物学的方法和工具被开发用于预测蛋白质-适配体相互作用。
这些方法可以分为两大类:基于结构的方法和基于序列的方法。
基于结构的方法主要依赖于蛋白质和配体的三维结构。
分子对接是最常用的方法之一。
分子对接是通过模拟蛋白质和配体之间的结合过程来预测它们的相互作用方式。
这种方法可以通过计算某些能量函数来评估不同的蛋白质-配体结合模型,并选择最稳定的模型作为预测结果。
除了分子对接,分子动力学模拟也是一种流行的基于结构的方法。
分子动力学模拟是通过模拟蛋白质和配体的原子运动来研究它们之间的相互作用。
通过分析模拟结果,可以获得关于结合位点、结合能力和结合机制等信息。
基于序列的方法主要基于蛋白质和配体的氨基酸序列信息。
这些方法常常使用机器学习算法来进行预测。
常用的机器学习算法包括支持向量机、随机森林和深度学习等。
这些方法可以通过分析大量已知的蛋白质-配体相互作用数据来学习模型,并用来预测未知的相互作用。
还有一些其他的方法,如药物虚拟筛选和结构基因组学等。
药物虚拟筛选是通过研究大量化合物的结构和生物活性数据,来预测新药物与蛋白质的相互作用。
结构基因组学是通过比较结构相似的蛋白质的特征和功能,来预测蛋白质-适配体相互作用。
蛋白质-适配体相互作用预测是一项重要的生物医学研究课题。
利用基于结构和序列的方法、机器学习算法、药物虚拟筛选和结构基因组学等技术,可以帮助科学家们更好地理解蛋白质-适配体相互作用的原理,并为药物设计和疾病治疗提供重要的参考和指导。
日本科学家揭示酸味的独特感觉机理
日本科学家揭示酸味的独特感觉机理佚名【期刊名称】《生物学教学》【年(卷),期】2009(34)2【摘要】据东方网2008年6月17日援引《科技日报》消息,日本自然科学研究机构生理学研究所的科学家发现,在人类舌头所能感觉到的五种味觉中,唯独酸味与甜味、辣味、咸味及苦味不同,具有其独特的感觉机理。
日本科学家在舌头感觉细胞的表面发现了两种分别称为PKD1L3 及PKD2L1的物质,它们均由蛋白质组成。
在这两种物质的作用下,舌头上的感觉细胞在接触到酸后不会立即反应,而是在酸味被唾液稀释、酸味刺激结束后才开始反应。
【总页数】2页(P72-73)【关键词】日本科学家;酸味;《科技日报》;科学研究机构;蛋白质组成;研究所;生理学【正文语种】中文【中图分类】Q5【相关文献】1.我国科学家破解SARS病毒进化规律·我国科学家揭示艾滋病发病新机理·俄美合成两种新化学元素·我国研制出纳米“超级开关”材料 [J],2.会发电的太阳能"布料"·科学家证实中微子质量·美国开发"非脂肪化"食品·我国新一代互联网关键技术获重大突破·日本实现半导体结晶光控制·科学家发现阻止衰老新法·俄发明抗癌新疗法·科学家揭示肝炎癌变秘密·私人载人太空飞船飞行成功 [J],3.意医生利用体外手术清除肝肿瘤/日本学者发现形成精子的关键基因/意大利科学家研制艾滋病新疗法/美研究揭示胚胎着床机理 [J],4.美国科学家找到人类感觉酸味的接受器 [J],5.日本科学家揭示类风湿性关节炎的致病机理 [J],因版权原因,仅展示原文概要,查看原文内容请购买。
医学英语写作与翻译
第三部分医学英语的写作任务一标题的写作(Title)标题的结构1. 名词+介词Blindness(视觉缺失)after Treatment for Malignant Hypertension 2. 名词+分词Unilateral Neurogenic Pruritus Following Stroke中风后单侧神经性瘙痒3. 名词+不定式Suggestion to Abolish Icterus Index Determination(黄疸指数测定)where Quantitative Bilirubin Assay(胆红素定量)is Available建议能做胆红素定量的化验室不再做黄疸指数测定4. 名词+同位语Gentamicine, a Selelctive Agent for the isolation of Betahemolytic Streptocc ociβ-溶血性链球菌庆大霉素是分离β-溶血性链球菌的选择性药物5. 名词+从句Evidence that the V-sis Gene Product Transforms by Interaction with the Receptor for Platelet-derived Growth Factor血小板源性生长因子.V-sis 基因产物由血小板生成因子受体相互作用而转化的依据6. 动名词短语Preventing Stroke in patients with Atrial Fibrillation心房纤维性颤动心旁纤颤患者中风预防Detecting Acute Myocardial Infarction(急性心肌梗死)byRadio-immunoassay for Creative Kinase(酐激酶)用放射免疫法测定酐激酶诊断急性心肌梗死7. 介词短语On Controlling Rectal Cancer8. 陈述句Dietary Cholesterol is Co-carcinogenic协同致癌因素for Human Colon Cancer9. 疑问句Home or Hospital BirthsIs Treatment of Borderline Hypertension Good or Bad?注意副标题的作用1.数目:Endoluminal Stent-graft 带支架腔内搭桥for Aortic Aneurysms动脉瘤: A report of 6 cases带支架腔内搭桥治疗动脉瘤的六例报告2.重点:Aorto-arteritis 大动脉炎Chest X-ray Appearance and Its Clinical Significance大动脉炎胸部X线表现及临床意义3.方法:Gallstone Ileus(胆结石梗阻): A Retrospective Study 4.作用:Carcinoembryonic Antigen in Breast-cancer Tissue: A useful prognostic indictor乳腺癌组织中癌胚抗原——一种有用的预后指示5.疑问:Unresolved—Do drinkers have less coronary heart disease? 6.连载顺序:Physical and Chemical Studies of Human Blood Serum: II. A study of miscellaneous Disease conditions人类血清的理论研究:II. 多种病例的研究7.时间:A Collaborative 综合Study of Burn Nursing in China: 1995-1999常见标题句式举例1. 讨论型:Discussion of/ on; An approach to; A probe into; Investigation of; Evaluation of / on汉语中的“初步体会”、“试论”、“浅析”之类的谦辞可以不译。
蛋白质结合自由能计算的统计力学模型建立
蛋白质结合自由能计算的统计力学模型建立在生物化学和生物物理学领域,蛋白质结合自由能是一个重要的研究课题。
准确地计算蛋白质结合自由能可以帮助我们理解生物分子相互作用的机制,并为药物设计和生物工程提供重要的指导。
在这篇文章中,我们将讨论一种基于统计力学的模型,用于计算蛋白质结合自由能。
首先,我们需要了解什么是蛋白质结合自由能。
蛋白质结合自由能是指在一个溶液中,两个分子结合形成复合物时,所涉及的能量变化。
这个能量变化不仅包括蛋白质和配体(或其他结合分子)之间的相互作用能,还包括溶剂效应和热力学参数的贡献。
因此,准确地计算蛋白质结合自由能是一个复杂的问题。
为了解决这个问题,统计力学提供了一个可行的方法。
统计力学是一种基于分子尺度的理论,通过考虑分子的运动和能量的分布,来描述宏观系统的性质。
在计算蛋白质结合自由能时,我们可以使用统计力学模型来估算不同构象之间的能量差异。
下面将详细介绍几种常用的统计力学模型。
第一种模型是配分函数模型。
配分函数是一个能够描述分子在不同能级上的分布情况的参数。
在配分函数模型中,我们将蛋白质和配体看作是一个多能级系统,每个能级对应不同的结构或构象。
通过计算配分函数,我们可以得到蛋白质和配体在不同构象下的能量分布,从而计算结合自由能。
第二种模型是自由能表面模型。
自由能表面是描述系统自由能随着不同变量(比如构象或配体的位置)变化而变化的函数。
在自由能表面模型中,我们通过建立系统的自由能表面来计算结合自由能。
这个自由能表面可以用不同形式的势能函数来表示,如二次函数或分段函数。
通过最小化自由能表面,我们可以找到系统的最稳定结构和对应的结合自由能。
第三种模型是分子动力学模拟。
分子动力学模拟是一种基于牛顿力学的模拟方法,通过模拟分子的运动轨迹来研究分子体系的性质。
在计算蛋白质结合自由能时,我们可以使用分子动力学模拟来模拟蛋白质和配体之间的相互作用。
通过统计模拟结果,我们可以计算结合自由能。
除了上述模型,还有其他一些方法可用于计算蛋白质结合自由能,如基于机器学习的方法和量化构效关系模型。
常用蛋白质相互作用研究技术的种类及基本原理
常用蛋白质相互作用研究技术的种类及基本原理蛋白质相互作用的本质其实是三种力,氢键,分子间作用力(范德华力)和疏水力,因为这三种力的作用距离都非常的短,所以相互作用的蛋白我们通常认为它们必定相互接近。
荧光共定位,在过去,这个技术一般用于细胞内辅助证明蛋白相互作用,前些年,如果是其他物种的蛋白质,你应用酵母双杂交系统验证了它们的相互作用,可能是假阳性。
白融合表达于原物种细胞当中,在高分辨显微镜下,如果两种荧光出现在同一位置,那么就证明它们空间上较为接近,很有可能产生了相互作用。
该研究方法首先将TAP 标签整合于该蛋白质的一端,标签由一个钙调蛋白结合多肤(CBP)与蛋白标签组成,并将 TEV 蛋白酶切位点插入二者之间,之后用带有TAP 标签的基因置换内源的蛋白基因并表达,且可与特定蛋白进行识别和结合裂解细胞,提取细胞总蛋白,并将所获总蛋白加入 IgG 亲和柱。
亲和柱上的 IgG 可与TAP 标签的ProA 端特异性结合,之后用洗脱液洗脱大多数非特异性结合蛋白,依次在洗脱液(合TEV 蛋白酶)洗脱和钙离子的协助下,获得高纯度的目的蛋白复合体。
经上述步骤所得的蛋白质复合体再进行SDS-PAGE 电泳分离及质谱分析,进而可发现其中的新组分或新蛋白复合物。
此种研究方法不仅能保持复合物结构的完整性,并且能够得到纯度较高的特异性。
因该技术的灵敏性、可靠性和特异性都优于传统的
酵母双杂交技术,尤其适用于研究蛋白质在生理条件下的相互作用。
但是,该技术在对高等真核细胞进行研究时却因原位蛋白标记难在真核细胞内进行,且易受内源蛋白的干扰等因素而具局限性。
蛋白质-适配体相互作用预测的方法
蛋白质-适配体相互作用预测的方法在细胞内部,蛋白质与其他分子之间的相互作用是一个非常重要的过程。
其中,适配体相互作用是一种特殊的相互作用,指的是一个蛋白质与其结合的小分子(适配体)之间的相互作用。
适配体相互作用在许多生物学过程中都扮演着至关重要的角色,例如代谢途径、信号转导、细胞增殖等。
因此,通过预测蛋白质-适配体相互作用对于药物发现和治疗疾病具有重要意义。
目前,已经发展出了许多蛋白质-适配体相互作用预测的方法,这些方法主要可以分为基于结构的方法和基于序列的方法两类。
以下将分别介绍这两类方法的原理和优缺点。
一、基于结构的方法基于结构的方法是利用已知结构的蛋白质和适配体来预测其相互作用的方法。
这类方法常用的工具包括分子对接软件、分子动力学模拟和药物虚拟筛选等。
具体而言,分子对接软件是目前最常见的蛋白质-适配体相互作用预测工具之一。
该方法是通过计算蛋白质和适配体之间的互作能,来预测它们的相互作用情况。
其中,互作能包括静电互作能、范德华互作能和氢键互作能等。
最终,该方法能够得到蛋白质和适配体的结合模式和结合能力等信息,从而为药物发现和设计提供重要的参考。
虽然基于结构的方法预测准确性较高,但由于需要先获得蛋白质和适配体的三维结构信息,因此该方法不适用于没有已知结构的蛋白质或适配体。
相比于基于结构的方法,基于序列的方法更注重蛋白质和适配体序列的分析。
目前,基于序列的方法主要有两种策略:一种是通过蛋白质和适配体序列的物化性质,如氨基酸属性、亲和性和分子排列,来预测它们之间的相互作用;另一种是通过利用已知的蛋白质-适配体结合数据集来训练机器学习模型,从而预测新的蛋白质-适配体相互作用。
在这两种方法中,基于机器学习的方法因其高效性和预测准确性而受到广泛关注。
例如,使用深度神经网络和卷积神经网络对蛋白质序列和适配体序列进行表示和分类,能够有效地预测它们之间的相互作用。
综上所述,蛋白质-适配体相互作用预测方法因其研究领域的重要性而备受关注。
蛋白质-适配体相互作用预测的方法
蛋白质-适配体相互作用预测的方法蛋白质-适配体相互作用是指蛋白质与其相互作用的小分子或其他蛋白质之间的相互作用。
这种相互作用在生物学中起着重要作用,因为它们可以影响蛋白质的功能、稳定性和活性。
准确地预测蛋白质-适配体相互作用对于药物设计和生物学研究具有重要意义。
在本文中,我们将探讨蛋白质-适配体相互作用预测的方法,并介绍目前主流的预测方法和技术。
蛋白质-适配体相互作用预测方法主要可以分为实验方法和计算方法。
实验方法包括X 射线晶体学、核磁共振和表面等等。
这些方法通常能提供高分辨率的结构信息,但是其在高通量预测上有一定的局限性。
相比之下,计算方法具有高效、低成本和可高通量的优势,并且在新药研发领域中得到了广泛应用。
目前,蛋白质-适配体相互作用预测的计算方法主要包括基于结构的方法、基于序列的方法和机器学习方法。
基于结构的方法利用蛋白质和配体的结构信息进行相互作用的预测,例如通过分子对接和蛋白质-蛋白质对接等方法。
这些方法通常需要蛋白质和配体的结构信息,因此对结构信息的质量要求较高。
由于组合爆炸和能量评分等问题,这些方法在大规模应用上存在一定的局限性。
除了上述方法,一些新的技术和方法也正在被应用于蛋白质-适配体相互作用的预测。
在人工智能和深度学习的帮助下,科学家们正在不断开发出新的模型和算法,以改善蛋白质-适配体相互作用的预测准确性和效率。
一些新的实验技术和生物信息学方法也被应用于蛋白质-适配体相互作用的预测,例如结合多种结构和序列信息的综合方法。
蛋白质-适配体相互作用预测是一个复杂而具有挑战性的问题。
随着计算方法和技术的不断进步,我们相信在不久的将来,我们将能够更加准确和高效地预测蛋白质-适配体相互作用,从而为药物设计和生物学研究提供更加有力的工具和方法。
蛋白质-适配体相互作用预测的方法
蛋白质-适配体相互作用预测的方法蛋白质-适配体相互作用是指蛋白质与其结合的小分子(适配体)之间的相互作用关系。
这种相互作用对于理解蛋白质的功能以及设计新的药物非常重要。
开发一种准确、快速和经济的方法来预测蛋白质-适配体相互作用对于药物设计和发现具有重要意义。
目前,已经开发了许多预测蛋白质-适配体相互作用的方法,其中包括基于结构的方法、基于序列的方法、基于机器学习的方法和基于模拟的方法等。
这些方法在预测蛋白质-适配体相互作用方面都各具优势和局限性。
基于结构的方法是通过分析蛋白质和适配体的结构信息来预测它们之间的相互作用。
这些方法通常基于蛋白质和适配体之间的分子对接模型,并利用分子对接算法来搜索最佳的结合位点和配对方式。
由于蛋白质和适配体的结构复杂多样,基于结构的方法面临着结构不确定性、计算复杂性和相关结构信息的获取等问题。
基于序列的方法是通过分析蛋白质和适配体的序列信息来预测它们之间的相互作用。
这些方法通常基于蛋白质的氨基酸序列和适配体的分子结构,利用生物信息学和机器学习技术来识别结合位点和预测相互作用强度。
尽管基于序列的方法可以快速预测蛋白质-适配体相互作用,但由于序列信息的局限性,其预测准确性和可靠性仍然有待进一步提高。
基于模拟的方法是通过分子动力学模拟等计算方法来模拟蛋白质和适配体的结合过程,从而预测它们之间的相互作用。
这些方法基于物理化学原理和计算力学模型,可以模拟蛋白质和适配体之间的精确结合机制和动力学过程。
基于模拟的方法通常需要大量的计算资源和时间。
预测蛋白质-适配体相互作用是个复杂而具有挑战性的问题。
目前的方法各有优势和限制,需要进一步的研究和发展来提高预测准确性和可靠性。
这将为药物设计和发现提供更多的有用信息,并加速新药的开发过程。
薛定谔显示氨基酸序列
第四篇示例:
薛定谔显示氨基酸序列是一种描述氨基酸序列或蛋白质结构的理论模型,其名称来源于著名的量子力学理论家薛定谔。在这个理论模型中,氨基酸序列或蛋白质结构被描述为类似于量子力学中的波函数,具有波粒二象性。
薛定谔显示氨基酸序列技术在生物信息学领域有着广泛的应用前景。通过该技术,生物学家可以更加高效地进行蛋白质序列比对和演化分析,从而为疾病诊断、药物设计和基因工程等领域提供有力的支持。薛定谔显示氨基酸序列技术还可以在生物大数据处理、量子计算和信息安全等领域发挥重要作用。
薛定谔显示氨基酸序列技术也存在一些挑战和限制。该技术的实验设备和计算资源要求较高,导致成本较高且操作复杂。薛定谔显示氨基酸序列技术在实际应相结合等。
不过,薛定谔显示氨基酸序列也存在一些挑战和限制。由于计算量大、计算成本高昂,目前这种方法还未得到广泛应用。对于大规模蛋白质结构的预测和设计,薛定谔显示氨基酸序列仍存在一定的局限性,需要进一步改进和完善。
薛定谔显示氨基酸序列是一种创新的技术,为生物科学研究和生物工程领域带来了新的思路和方法。随着技术的不断发展和完善,相信这种方法将会在未来发挥越来越重要的作用,为人类的健康和社会发展作出更大的贡献。【阿巴阿巴】。
薛定谔显示氨基酸序列
全文共四篇示例,供读者参考
第一篇示例:
薛定谔显示氨基酸序列是一种用量子力学的方法来预测蛋白质结构和功能的技术。这种方法以奠基人之一薛定谔的名字命名,旨在探索生物分子的微观世界。氨基酸是构成蛋白质的基本组成单元,其序列决定了蛋白质的结构和功能。
蛋白质构象的计算模拟
蛋白质构象的计算模拟介绍蛋白质是生命体系中具有重要生物学功能的一类大分子,也是生命科学研究的重要对象。
蛋白质的功能如何实现,主要与蛋白质的三维构象密切相关。
蛋白质的构象在很大程度上决定了其生物学功能,因此对蛋白质构象的计算模拟一直是生命科学研究中的重要任务。
计算模拟方法计算模拟方法是一种利用现代计算机对具有一定规律性的物质系统进行分子动力学计算模拟的方法。
计算模拟方法包括分子动力学模拟、蒙特卡洛模拟、分子机器设计等。
其中分子动力学计算模拟方法是目前应用最广的一种方法。
分子动力学模拟分子动力学模拟是一种利用分子速度和位移方程对体系进行计算和模拟的方法。
该方法计算的基本量包括原子的位移、速度、动量、能量和力等。
其中力是决定构象的关键因素,它对原子间的相互作用进行描述。
分子动力学模拟的计算方法既考虑了物体的微观力学特性,又考虑了宏观物质热力学特性。
蒙特卡洛模拟蒙特卡洛模拟是一种基于随机数的随机模拟方法。
蒙特卡洛模拟的主要过程是将体系状态随机变化,得到一组可能性极大的体系状态。
通过估算每一种状态的概率,得到体系各种状态的概率分布。
由于蒙特卡洛模拟计算的质量精度和计算量均可控制,因此在一些涉及到高精度计算和稀有事件分析中被广泛应用。
分子机器设计分子机器设计是指借鉴生物分子机体的结构及功能,采用化学合成、生物合成等方法制备大分子分子机器的技术。
在分子机器设计中,分子动力学模拟技术被广泛应用。
分子动力学模拟技术可以帮助研究人员理解生物分子机体的功能和结构,从而进行分子机器的设计、合成、构筑和改造,实现一些特定的消费、医药、安全、航空、军事、通讯等应用。
应用蛋白质构象计算模拟在生物科学、化学、材料学、计算机科学等领域均有广泛应用。
在生物科学中,蛋白质构象计算模拟主要用于研究蛋白质结构与功能之间的相互关系,预测蛋白质折叠路径及其稳定性,设计蛋白质的新功能和新构象等。
在化学和材料学中,蛋白质构象计算模拟主要用于模拟材料的性质,研究新材料的合成方法,分析材料的表面和界面等。
multiwfn计算解离能
multiwfn计算解离能解离能是指化学反应中,由于键的断裂而释放出的能量。
它是评价化学反应的重要指标之一,能够揭示反应的稳定性和反应动力学等信息。
而multiwfn是一种常用的计算化学软件,可以用于分析和计算分子的电子结构和性质。
本文将介绍如何使用multiwfn计算解离能。
我们需要准备一个包含反应物和产物的分子结构文件。
可以通过化学软件绘制或从实验数据中获取。
假设我们要计算的是H2分子的解离能。
接下来,我们需要使用multiwfn软件进行计算。
首先,打开multiwfn软件,选择"Calculate"菜单下的"Properties"选项。
然后,在弹出的窗口中选择"Energy",再选择"Energy difference between two fragments"。
接着,我们需要输入反应物和产物的分子结构文件。
在multiwfn软件中,选择"Input & Output"菜单下的"Input"选项,然后选择"Load Cartesian Coordinate"。
在弹出的窗口中,选择反应物和产物的分子结构文件。
接下来,我们需要指定分子中的原子序号来定义反应物和产物的分子片段。
在multiwfn软件中,选择"Define Fragment"菜单下的"Input"选项。
然后,在弹出的窗口中,输入原子序号来定义反应物和产物的分子片段。
接着,我们需要选择计算方法。
在multiwfn软件中,选择"Method"菜单下的"Energy"选项。
然后,在弹出的窗口中,选择适合的计算方法。
我们可以点击"Run"按钮开始计算解离能。
multiwfn软件将根据所选择的计算方法和分子结构文件,计算出反应物和产物的能量差,即解离能。
黄酮类化合物对抑制重组人蛋白激酶CK2全酶的二维定量构效关系
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caglioti反应机理
caglioti反应机理Caglioti反应机理是一种在化学和材料科学中广泛应用的理论体系,其基本原理是结合了分子动力学和量子力学的计算方法,用于描述材料中的晶体结构和分子运动。
该理论体系是由意大利化学家Caglioti在20世纪50年代提出的。
在晶体结构分析中,Caglioti反应机理用于确定晶体中原子或分子的位置和方向,以及它们的振动和旋转运动。
这种机理基于分子间相互作用的强度和距离,可以预测材料的物理和化学性质。
基于分子动力学的计算方法,Caglioti反应机理可以模拟材料中的分子运动。
通过计算分子的速度、轨迹和相互作用力,可以预测材料的热性质、光学性质和电子性质等属性。
该方法还可以研究分子之间的反应和化学反应机理。
Caglioti反应机理已经成为现代材料科学研究中的重要工具,尤其在材料模拟和计算领域中得到了广泛的应用。
在材料设计和优化中,利用该理论体系可以预测材料的结构、性质和性能,为实验研究提供有力支持。
Caglioti反应机理在材料中的应用涉及范围非常广泛,包括但不限于固体、液体、气体等。
在固体材料中,Caglioti反应机理可以解释晶格畸变和化学键能量的变化,帮助研究材料的力学性质、热扩散性质和热传导性质等。
在生物医学领域,Caglioti反应机理也得到了特别的关注。
该理论体系可用于预测生物分子的结构、功能和相互作用,从而为药物设计和生物材料研究提供有力支持。
在药物设计中,利用Caglioti反应机理可以计算药物分子和靶分子的结合能力,并预测药物分子的药效和毒性,从而为药物治疗提供合理依据。
Caglioti反应机理还可以应用于材料的制备和加工。
在纳米材料制备中,利用该理论体系可以探索纳米材料的生长机理和相变规律,为压电材料、光电材料、储氢材料等应用领域提供优质材料支持。
Caglioti反应机理也存在着一些局限性。
对于复杂的大分子材料,由于其分子量的巨大性,由于现有计算技术的限制,计算精度可能不足,需要采用一些近似计算方法来处理这些复杂问题。
蛋白质的β-发夹、β(γ)-转角及四类简单超二级结构预测的开题报告
蛋白质的β-发夹、β(γ)-转角及四类简单超二级结构预测的开题报告一、研究背景和意义蛋白质是生命体系中重要的分子,参与了各种生命过程,包括酶催化、细胞信号传导、免疫反应等。
蛋白质的功能是由其构象决定的,而蛋白质的构象又与其二级、三级甚至四级结构密切相关。
因此,预测蛋白质的二级结构对于理解蛋白质功能及其在生命体系中的作用具有重要意义。
β-发夹和β(γ)-转角是蛋白质中常见的二级结构,对于蛋白质结构的稳定性和功能具有重要作用。
而四类简单超二级结构包括β转子、β桥、α螺旋和γ转子,这些结构在蛋白质的稳定性和折叠过程中也起着重要作用。
因此,研究蛋白质的β-发夹、β(γ)-转角及四类简单超二级结构的预测不仅有助于理解蛋白质的结构和功能,也可以为相关领域的研究提供重要的参考依据。
二、研究内容和方法本研究将通过文献调查和学习相关算法,探讨一些主流的β-发夹、β(γ)-转角及四类简单超二级结构预测算法,包括但不限于以下方法:1. 基于氨基酸序列的预测方法:该方法主要是通过分析氨基酸序列中特定的组合模式,如亲水性、疏水性、电荷等特征,预测蛋白质的二级结构。
该方法的缺点是准确度较低,但是相对简单并且适用于各种类型的蛋白质。
2. 基于物理学模型的预测方法:该方法是基于对蛋白质二级结构物理学特性的研究,通过计算蛋白质的氨基酸间键能量、电荷、氢键等因素,预测蛋白质的二级结构。
该方法的优点是准确度较高,但需要大量计算和较复杂的模型。
3. 基于机器学习的预测方法:该方法通过训练机器学习模型来预测蛋白质的二级结构。
常用的机器学习算法包括随机森林、支持向量机等。
该方法的优点是能够处理大量的数据和复杂的信息,准确度也相对较高。
三、研究目标和计划本研究的主要目标是探究并总结β-发夹、β(γ)-转角及四类简单超二级结构预测算法的原理、特点以及它们的优缺点。
并尝试使用其中的一些方法,对已知蛋白质序列进行二级结构预测,评估其准确度。
具体研究计划如下:阶段一:文献调研和方法学习(5周)1. 细致阅读相关文献,了解蛋白质二级结构预测的现状和发展趋势;2. 学习和掌握常用的二级结构预测算法的原理和流程,包括基于氨基酸序列的预测方法、基于物理学模型的预测方法、基于机器学习的预测方法等;3. 了解蛋白质二级结构预测中的数据集划分、特征提取和模型训练等技术,为后续的实验打下基础。
分子生物学知识:蛋白质结构和功能的计算模拟研究方法
分子生物学知识:蛋白质结构和功能的计算模拟研究方法随着计算机技术和生物实验技术的迅猛发展,分子生物学研究逐渐向计算化、数字化方向转变,计算模拟成为了分子生物学研究的重要工具之一。
其中,蛋白质结构和功能的计算模拟研究方法,不仅可以帮助我们深入理解蛋白质的结构和功能,而且还可以为疾病的发现和治疗提供新的思路和方案。
一、蛋白质结构的计算模拟1.1能量最小化模拟蛋白质结构的计算模拟最基本的方法是能量最小化模拟。
它基于分子力学原理,通过计算蛋白质中原子之间的相互作用能量,寻找能量最低的蛋白质构象。
这种方法可以预测蛋白质的结构,验证实验结果,并且对疾病研究和药物研发提供指导。
1.2分子动力学模拟分子动力学模拟是一种可以模拟蛋白质在动态条件下的结构和功能的方法。
通过分子动力学模拟,可以研究蛋白质在不同环境下的变化、蛋白质与其他小分子的相互作用等重要问题,对于了解蛋白质在疾病、药物研发等方面的作用机制,具有重要意义。
1.3蒙特卡罗模拟蒙特卡罗方法是一种基于概率计算的模拟方法,在蛋白质结构研究中,主要用于寻找能量更低的构象和预测结构,因此在蛋白质折叠研究中有着广泛应用。
二、蛋白质功能的计算模拟2.1蛋白质与配体的相互作用模拟蛋白质与配体之间的相互作用在生物分子的信号传递、药物研发等方面具有重要意义。
计算模拟可以模拟不同配体在蛋白质结合的过程中与蛋白质之间的相互作用,研究配体在结合和解离过程中的结构和动力学变化,进而为药物的研发和生物分子的功能研究提供指导。
2.2蛋白质动力学模拟蛋白质的功能是在其具体的结构基础上实现的。
蛋白质的结构和功能不是静态的,而是经常发生变化。
因此,通过蛋白质动力学模拟,可以模拟蛋白质的运动和变形,研究蛋白质具体的功能,比如酶催化过程、离子通道开关机制、蛋白质分子的递交和传递等生理生化过程。
三、计算模拟方法在疾病研究和药物研发中的应用3.1疾病研究计算模拟可以帮助研究人员解决一些传统实验难以解决的问题,比如人类疾病的发病机制、病毒感染机制等。
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Calculi for InteractionRobin MilnerCambridge,April1995 Abstract Action structures have previously been proposed as an algebra for both the syntaxand the semantics of interactive computation.Here,a class of concrete action structures calledaction calculi is identified,which can serve as a non-linear syntax for a wide variety of modelsof interactive behaviour.Each action in an action calculus is represented as an assembly ofmolecules;the syntactic binding of names is the means by which molecules are bound together.A graphical form,action graphs,is used to aid presentation.One action calculus differs fromanother only in its generators,called controls.Action calculi generalise a previously defined action structure PIC for the-calculus.Sev-eral extensions to PIC are given as action calculi,giving essentially the same power as the-calculus.An action calculus is also given for the typed-calculus,and for Petri nets parametrizedon their places and transitions.An equational characterization of action calculi is given:each action calculus is the quotientof a term algebra by certain equations.The terms are generated by a set of operators,includingthose basic to all action structures as well as the controls specific to;the equations are thebasic axioms of action structures together with four additional axiom schemata.1IntroductionBackground There is a remarkable variety among basic calculi for computation.Perhaps the most familiar,at least the most commonly known as a“calculus”,is the-calculus.But other oper-ational models–Turing machines,register machines,recursion equations,...–also deserve to be called calculi;in each case there is a formalism,and some rules and metatheory about the construc-tion and combination of terms in the formalism.The variety is such that we cannot claim a clear understanding of the family of all such calculi,even though an underlying theory of functions has been developed which gives them semantic unity.When“computation”is expanded to include concurrent or interactive behaviour,we cannot rest only upon the intuitions of such a theory in formulating a calculus.As a consequence,there is even greater variety among calculi which describe interactive systems.(Examples are:Petri nets,many process algebras,communicating automata,statecharts,....)So perhaps we have even less hope of classifying them.Yet it may not be so;since the population of calculi is larger,repeated features among them may be more apparent.By giving attention to interaction as a fundamental notion,we may reveal regularities not hitherto detected.The need for some classifying discipline is all the greater,since the generalisation from compu-tation to interaction is also a move from prescriptive to descriptive.In the world of networks and distributed computing we cannot claim that all the systems we study are built to a prescription;in-stead,we seek a descriptive theory to analyse the phenomena of an ever more complex informatic world,which is partly“natural”and partly man-made,and in which computation is a special case.A taxonomy of models of interaction will be a step towards such a theory.1Motivation and character In this paper a mathematical framework is proposed for studying, comparing and combining operational models of interaction.Each such model appears in the frame-work as an action calculus;action calculi are a special class of action structures[15],and each mem-ber of the class is determined by its generators,called controls.Two different characterizations of action calculi are given,and several examples of action calculi are presented.The paper prepares the way for the common treatment of the semantic interpretations of all ac-tion calculi,via homomorphisms of action structures;this will be pursued in later papers.One par-ticular aim is tofind a general treatment of behavioural equivalences such as bisimilarity.Another aim is to classify action calculi according to their dynamic qualities;for example,the-calculus has been called a calculus of mobile processes,and we would like to say precisely what is meant by mobility.The next few paragraphs give some general motivation for action calculi,and roughly explain their character.If we consider Petri nets[20],CSP[7]and the-calculus[19]beside the-calculus[2],we find recurrent features.The parallel composition of CSP looks like the juxtaposition(with some transition-sharing)of Petri nets;exact translations between the two have been made on this basis. The-calculus has binding of names,begging comparison with the richer notion of bound variable in the-calculus.Parallel reduction of a term of the-calculus,in the presence of a shared valuation of the free variables,is somewhat like the interaction between several independent agents and a shared resource;such interactions are well-represented in Petri nets.Finally,the dynamic rules of such models are often expressed in a similar way:the reduction of,or reaction within,certain key control configurations(called redexes in-calculus,andfireable transitions in Petri nets).Of these common features,the use of names is one of the most crucial,and presents a funda-mental challenge.The problem is that names are used in different ways.In the-calculus they are variables which may be replaced by any value(or term denoting a value);in the-calculus they are channels,and also variables–but only over channels;in Petri nets they are sometimes used to identify transitions(but not as variables over transitions).The solution adopted here is that names, even when variables,may only stand for names.Thus we have separated the two attributes of a name which are combined in-calculus(and often treated as inseparable!);a name may vary,and it may denote a value.in action structures we take varying as basic,and represent it by an abstrac-tion operator;denoting can be treated as a special case of interaction,as will be seen in Section5.5 where the-calculus is presented.The basic ingredients of action structures–composition,tensor product,abstraction and a re-action relation–were chosen as a minimum to provide a uniform treatment of features common to many calculi.(The mathematical structure defined by these ingredients alone may be too weak to be of independent interest;action structures should be considered mainly as a basis for the enrich-ments introduced here.)In addition,action calculi provide a uniform way to introduce specific con-trol mechanisms;behaviour is represented by interaction between the members of certain control configurations.The framework hardly limits the variety of such control disciplines;but it allows us to ask what happens if we combine them.For example,can we enrich Petri nets by allowing them to change configuration dynamically?We can formulate this enrichment precisely as the combination of the controls of two action calculi:Petri nets and the-calculus.The action structure framework was designed to accommodate not only the syntax(operational models)but also the semantics(abstract models)of interactive behaviour.In[15]was given an ex-2ample expressing the meaning of a simple calculus as a homomorphism between two action struc-tures,one expressing the evaluation of expressions and the other containing the denoted values. Since we wish to extend this treatment to calculi in general,wefirst have to determine the class of action structures which can be considered as calculi.Technical overview A standard way to set up a calculus is to define a term algebra,and then pro-vide it with reduction rules or transition rules.But for interactive systems it has been found helpful to use a formalism richer than a term algebra.Following ideas of Banˆa tre and M´e tayer[4],Berry and Boudol based their Chemical Abstract Machine(Cham)[3]on the notion of multiset.Prompted by them,the present author imposed a structural congruence upon the-calculus as part of the for-mal language,not of the semantics[14].Again,Meseguer and Montanari[10]have revealed the monoidal structure inherent in Petri nets.Indeed,part of the reason for the success of Petri nets is that its syntax,being graphical,reflects this structure.Action structures impose monoidal structure.In fact they go further;they include the operation of abstraction(parametrization)over names,and also represent dynamics as a preorder.Both the monoidal and the additional structure are characterized by algebraic axioms.Let us outline how an action calculus is defined as the quotient of a term algebra.We begin with the operators of action structures,and arrive at action calculi by three further steps.Thefirst step is to introduce naming constants;these give power to an action structure to manipulate names, which act as the“wiring”or connective tissue for all action calculi.Four equational axioms called naming axioms are imposed upon the naming constants.Thisfirst step is common to all action calculi.The next step is specific to each action calculus:we supply a family of control operators, or controls,together with a set of control rules which define the reaction relation.Thefirst two steps yield a term algebra defined by all these operators;thefinal step is to quotient this term algebra by the action structure and naming axioms.These quotient algebras also have an appealing concrete presentation;each action can be considered as a structure of molecules in the spirit of the Cham.An action structure PIC,corresponding to a fragment of the-calculus[16],was described in[15];it nowfinds its place as an action calculus with just three generators;(restriction),in (input)and out(output).An action calculus for Petri’s place-transition nets is generated by,pre (pre-condition),post(post-condition)and m(marking).Thus action calculi begin to achieve one of the aims of action structures–to unite different models of concurrency in a common setting.The action calculus concept goes beyond what was achieved in[15].That paper failed to express a full-fledged process calculus as an action structure(PIC falls short of the full-calculus,since it lacks the prefixing,summation and replication constructions);instead,it showed how to build a process calculus on top of an arbitrary action structure.We show here that this further structure is redundant;process calculi can be exhibited as action calculi.Organisation of the text The main technical definitions and results of the paper appear in Sec-tions4and6;the remaining sections supply background,motivation and examples.The paper is organised as follows.Section2reviews the basic definition of action structures.Section3reviews the action structure PIC,an exemplar for the general definition of action calculus.Section4de-fines action calculi formally in terms of their concrete presentation,molecular forms;a graphicalpresentation called action graphs is also defined.Section5gives a series of examples of action cal-culi;itfirst shows how PIC can be extended to richer action calculi by adding further generators, then presents both the typed-calculus and Petri nets as action calculi.Action graphs are freely used,especially to present control rules.Section6gives formally the algebraic characterization of action calculi;it demonstrates that each action calculus is isomorphic to the quotient of a term alge-bra by the action structure axioms together with four further axiom schemata.Section7identifies some further lines of investigation;in particular,it sketches the recently discovered control struc-tures[12].A control structure is an action structure with additional structure;each set of controls equipped with dynamic rules determines not only an action calculus but also a category of control structures in which the action calculus is initial;these control structures are therefore semantic in-terpretations of the action calculus.Acknowledgements I owe much to intense discussions with Yoram Hirshfeld,around Christmas 1993.He helped me to explore many paths,attractive and thorny;many were cul-de-sacs,but the exploration contributed to the present ideas.I thank Adriana Compagnoni,Philippa Gardner,Ole Jensen,Benjamin Pierce,John Power and Peter Sewell,for many suggestions which have improved the paper.2Action structures reviewedIn this section we recall from[15]the basic notion of an action structure.Wefirst give it in category-theoretic terms,then elaborate it algebraically.A little familiarity with the notion of monoidal cat-egory will help the reader,but no further knowledge of categories is needed.2.1Definition(Action structure)A(dynamic)action structure is a strict monoidal category, with two extra items:-a set referred to as names,and for each an endo-functor upon known as an abstractor;-a preorder over each hom-set of,called reaction,which is preserved by composition, monoidal product and abstraction,and for which the units are minimal.If the preorder is the identity relation,or is not supplied,is called a static action structure.For each pair of arities possesses,second,a family of actions;they are the mor-phisms of as a category.If is a member of this set we write and call and the source and target arities of;we even abuse terminology by calling just the arity of.We shall use to range over actions.Third,since is a monoidal category with abstractors,there is a unit action id for each arity,the operations of composition,tensor or monoidal product,and an abstraction operator ab for each.They obey the following arity rules:id3An action structure for the-calculusIn this section we define an action structure PIC,corresponding to a fragment of the-calculus.It is studied more fully in Part II of[15].Here we shall use it as an exemplar and motivation for the definition of action calculi to be given in Section4.We take the arities of PIC to be N–the natural numbers under addition.3.1Particles PIC formalises two basic features of the-calculus;the passage of names through ports which are also names,and the localisation of names by restriction.The constituents of an action in PIC are the particles,given by()representing the receipt of a name followed by its use as a port.Thus thefirst occurrence of binds the second.Adopting the convention that the scope of a binding extends to the right,we therefore declare the body of an action to be a partial sequenceof particles;that is,a sequence in which we allow the commutation of any adjacent pair, if neither binds a name occurring in the other.An action is a particle form()where is an-vector of distinct names,the imported names,and is an-vector of names(not necessarily distinct),the exported names.The imported names in a particle form are bound.The scope of each bound name–either imported or bound by a particle–extends to the right of its binding occurrence,and includes the exported names.We identify actions which only differ by alpha-conversion(change of bound names).For clarity,we may enclose a sequence in square brackets.As an example,let()()then the composite will impose the substitution upon the body of,yielding()()We now define all the action structure operations for PIC.63.3Operations First,the identities are given byid def()We shall apply substitutions like,where is a vector of distinct names,to various syn-tactic forms;;is the result of simultaneously replacing each free occurrence of in by the corresponding,first alpha-converting to change any bound uses of.Note that only a name can replace a name;we do not use the general form of substitution in which arbitrary terms replace variables.Composition,product and abstraction are given as follows,where we assume(), ()and that neither binds a name occurring in the other:def()def()ab def()Thus is simply the juxtaposition of the two actions;no order is dictated by the concatenation of the bodies,since the convention ensures that in this case.But in the substitution may replace some names free in by names bound in,and then.It is a routine matter to verify the action structure axioms.3.4Dynamics The reduction relation of PIC is defined as follows.Whenever contains a subsequence like()(after suitable commutations),we have()where is the substitution.We call()()()Note that has two reductions,even though and alone have none.Note also that the port of a redex(in the example,first then)may be free or bound.In contrast,consider:()()In this case,both and contain redexes,so we have()and(). In there is no requirement that react before,so we have two reaction sequences:()()This illustrates the point made in2.3that composition represents dataflow,not sequential compo-sition.One can check that is preserved by the operations;for example implies. The reaction relation is defined to be,the transitive reflexive closure of reduction.73.5Discussion PIC has considerable expressive power;for example it encodes the linear-calculus naturally,mimicking-reduction by reaction.The encoding is along the lines of[14].But PIC needs to be extended if it is to be a practically useful calculus of processes.The extensions to PIC defined in Section5below provide at least the expressive power of the original-calculus, while remaining entirely within the framework of action structures.We shall now show how PIC,though apparently quite specific,is an instance of a more general construction.We begin by showing how all actions with empty bodies can be generated.3.6Naming actions We call the following actions naming actions:def()def()It is easy to show that every action(),with an empty body,can be expressed in terms of naming actions via the action structure operations as defined in3.3.For example,()abThese body-free actions are just concerned with wiring;they form the export vector from the import vector by copying,permuting and discarding.3.7Control constants Each particle of PIC may have some free and some binding occurrences of names.Indeed,if we ignore dynamics,the only difference among the three kinds of particle is in the number of free and bound names they carry.We therefore reveal the generality of particle formation more clearly if we simply declare that there are(for PIC)three control constantsoutinand that for any control constant there are particles of the form()where the names are distinct and binding.Thus our three forms of PIC particle,It is now easy to show that every action in PIC is expressible in terms of the naming actions and control constants,via the action structure operations.Moreover,the dynamics of PIC is elegantly expressible in these terms.Let us defineout def id outin def inthen it can be verified that the reaction relation for PIC given in3.4is the smallest preorder preserved by the action structure operations,and obeying the ruleout in idThus we see clearly what is specific to PIC:its set of control constants,their arities,and their dy-namics as expressed by the above rule.In a similar way we may define a wide variety of action structures,each one determined by a given set of control constants and a set of dynamic rules called control rules which determine their meaning.According to Definition4.12to follow,each action structure built in this way(with reaction rules also given for)is an action calculus,denoted by AC().PIC=AC(out in)is just a special case of this uniform construction.However,the action calculi generated in this way are not sufficiently general;they lack an im-portant control feature.In these calculi,if is a possible reaction,then it may occur in any context;there is no way to delay it until some other activity is complete,or to make it conditional on the outcome of that activity.Definitions4.4and4.12will remove this deficiency.4Controls and molecular formsIn this section we formally define a class of action structures which we shall call action calculi. Their actions are more general than the particle forms discussed in the preceding section;in fact a particle()is a special case of a richer construction which we shall call a molecule.This notion of molecule is similar to that of Berry and Boudol[3];one difference is that our molecules can bind one another,since a molecule is a name-binding operator.The molecules of any action calculus are formed from generators which we shall call control operators,or simply controls.A control operator is a generalisation of the notion of control constant;its purpose is to control the activity of subactions.An example is the simple guarding construction of CCS;cannot act until has happened.Sequential composition in CSP is another example;cannot act until hasfinished mbda abstraction in the lazy-calculus is a third example;the redex must be reduced before is reducible.An action calculus will be determined by a set of controls,which we call a signature,together with a set of control rules which we shall define later.We let range over controls.4.1Definition(Control)A control is an operator which allows the construction of an actionfrom a sequence of actions,subject to a rule of arity having the following form:9An example of a signature is out in;with appropriate arity rules and control rules it determines PIC,presented formally in Section5.1.Its controls all have rank0;that is,they are control constants.Another example is ap,where has rank1;in Section5.5we see that it determines the-calculus(either simply typed or type-free,depending on the arity monoid).From now on we assume afixed denumerable name-set.We also impose a constraint upon the monoid of arities of an action calculus,bearing in mind its operational purpose.We require that be freely generated by a set of prime arities,,...,and that names be associated only with prime arities,infinitely many names with each prime.We are now ready for ourfirst presentation of action calculi,in terms of syntactic constructions known as molecular forms.4.2Definition(Molecules and molecular forms)Let be a signature.The molecular forms over are syntactic objects;they consist of the actions defined as follows,in terms of molecules :()()Molecules are binding operators.In the above molecule,the names occur free;they are the means by which it is bound into an action.In the above action,any name-vector in round brackets–either at the head of or at the right end of a molecule in–is binding,and its scope extends rightwards to the end s which are not thus bound are free in.We write fn for the free names of.Alpha-conversion of bound names is allowed.We assume that no name has more than one binding occurrence in any molecule or action.In above,are called the imported names and the exported ones.The body, sometimes written,is a possibly empty partial sequence of molecules,in which any two adjacent molecules may be commuted if neither binds a name occurring free in the other.an arc is drawn from the source which binds it;each free occurrence of a name is labelled by the name.Here is the graph which represents the example displayed above:These operations are easily represented graphically.We shall not define the operations on graphs formally,but just suggest them to the reader as follows:id abIn constructing the graph of ab,an arc is taken from the new source(shown)to each sink labelled in,and the label is removed(shown as).It is easy to establish the following,justifying our definition:4.5Proposition With the operations of Definition4.4,AC is a static action structure.4.6Definition(Naming actions)The datum(for each name)and the discard are actions defined as follows:def()def()It is now easy to establish4.8Proposition(Generation)All actions in AC can be defined using data,discard and con-trols together with the action structure operations.Indeed this is suggested by our action graphs;in the graph for ab,if is not free in then no arcs are added in addition to the horizontal one.We now introduce reaction rules,in order to provide the dynamics of molecular forms.124.11Definition(Control rule)A control rule over a signature takes the formwhere and are terms built from metavariables using data,discard and controls together with the action structure operations.Note that AC is essentially AC(,).When is understood,we often write AC()to mean AC().We have seen that the reaction relation of PIC=AC(out in)is generated by the control ruleout in idwhere out id out and in in;that is,it is the smallest preorder preserved by the action structure operations which satisfies this rule.Expressed in molecular form,the control rule of PIC is()out in()()It may also be presented graphically:........................outinidThe controlling power of controls(not of rank0)is due to the fact that a reaction relation need not be preserved by controls;e.g.we may have but not.Control mechanisms of arbitrary complexity may be introduced into action calculi;we do not expect to postulate a basic family of controls which is in some sense complete.But the action calcu-lus framework can save work in setting up calculi for interaction,since only the controls need to be specified–and indeed may be shared among the calculi.It also allows us more readily to compare and classify such calculi,on the basis of their controls and associated dynamic rules.We conclude this section by mentioning briefly the simplest action calculus of all.134.13The trivial action calculus The simplest action calculus is AC().It consists just of body-free molecular forms(),with the identity relation as reaction relation.Proposition4.8asserts that it is generated by the naming actions together with the action structure operations.The graph-ical forms contain no ovals(molecules);they are just“wiring”.We may think of AC()as the connective tissue which we use to build more interesting action calculi;we present several exam-ples of these in the following section.5Examples of action calculiWe start this section with a review of PIC,which is just AC(out in).This is the essential-calculus,as it contains no more than the basic controls for restriction and name-passing.Then we enumerate a sequence of fragments of-calculi,with additional controls:boxing(which may also be called guarding),choice and replication.These all come into-calculus as defined in[13],and together they appear to provide the same expressive power.We continue with an action calculus for the-calculus in5.5,and conclude the section by outlining an action calculus of Petri nets in 5.6.In most cases we use action graphs to illustrate the control rules.In one case,the-calculus with boxing,we state a theorem which asserts that the action calcu-lus represents,in a precise sense,the fragment of the-calculus to which it corresponds.Similar theorems are believed to hold in the other cases.Our presentation in each case is quite brief,since(once the arities are defined)each action cal-culus is determined just by its controls and their dynamics.For PIC and its extensions,we take the arities to be the natural numbers.For the-calculus and Petri nets we need a little more structure on the arities.5.1Basic-calculus:PIC=AC(out,in)Controls out in(rank0)Arity rulesout inDerived controls out def id outin def inControl rule out in idOne might have expected the control rule to be stated in the formout inbut in fact these two rules generate the same reaction relation,because of the closure conditions.In Section4.4we presented this control rule in graphical form.145.2-calculus with boxing:AC(out box)We now present a more realistic fragment of the-calculus.In order to emphasize that the repre-sentation is precise,we shall present the calculus and its reduction rulesfirst as a process calculus in the style of[13],then as an action calculus.Finally,we state a proposition which asserts that the latter is a faithful representation of the former.The terms of the process calculus are.It was introduced by Honda and Tokoro[8],who show that output guarding can in fact be defined in terms of input guarding.As in[13],wefirst define a structural congruence relation over process terms,by the follow-ing equations:whenever is alpha-convertible to()()()()()()(not free in)Then the reduction relation over terms is the smallest closed under structural congruence which obeys the following rules:COMMRESboxDerived controls out def id outbox def boxControl rule out boxIt is clear that in is redundant in the presence of box,as it is essentially box id.In Section4.12we presented the simpler rule out in id both in molecular form and graph-ically.To show the correspondence,let us do the same for the box rule.In molecular form it is()out box()15。