научная статья по теме QUANTUM CHEMISTRY, PHYSICAL CHEMISTRY, MOLECULAR DYNAMICS SIMULATION, DFT (DENSITY FUNCTIONAL THEORY), AND COARSE-GRAINING TECHNIQUES APPLIED IN STRUCTURAL, CELLULAR BIOLOGY, POLYMER SCIENCE AND IMPLICATION FOR SCALEPORTATION Комплексное изучение отдельных стран и регионов

Текст научной статьи на тему «QUANTUM CHEMISTRY, PHYSICAL CHEMISTRY, MOLECULAR DYNAMICS SIMULATION, DFT (DENSITY FUNCTIONAL THEORY), AND COARSE-GRAINING TECHNIQUES APPLIED IN STRUCTURAL, CELLULAR BIOLOGY, POLYMER SCIENCE AND IMPLICATION FOR SCALEPORTATION»

НАНОСТРУКТУРЫ

NANOSTRUCTURES

Статья поступила в редакцию 28.02.11. Ред. рег. № 951 The article has entered in publishing office 28.02.11. Ed. reg. No. 951

PACS 87.10.-e 87.16.A- 87.16.-b 82.35.Pq 82.35.Lr 82.70.-y 34.10.+x 46.05.+b

КВАНТОВАЯ ХИМИЯ, ФИЗИЧЕСКАЯ ХИМИЯ, МОЛЕКУЛЯРНАЯ ДИНАМИКА, ФТП (ФУНКЦИОНАЛЬНАЯ ТЕОРИЯ ПЛОТНОСТИ)

И МЕТОД ОГРУБЛЕННОГО ОСРЕДНЕНИЯ, ИСПОЛЬЗУЕМЫЕ В СТРУКТУРНОЙ, КЛЕТОЧНОЙ БИОЛОГИИ, НАУКЕ О ПОЛИМЕРАХ, И ПРИМЕНЕНИЕ ДЛЯ ПЕРЕНОСА

ПО МАСШТАБАМ

1 1 2 В. С. Травкин , Н.Н. Болотина '

hierarchical Scaled Physics and Technologies (HSPT), Los Angeles, CA, USA E-mail: travkin@travkin-hspt.com 2University of Applied Sciences, Rheinbach, Germany

Заключение совета рецензентов: 15.03.11 Заключение совета экспертов: 23.03.11 Принято к публикации: 25.03.11

В известной нам вселенной не существует веществ с физическим объемным содержанием, которое одновременно не являлось бы гетерогенным. Вопрос заключается в том, на каком масштабе (уровне) вещество становится таковым - на атомном, планетарном, звездном, уровне субчастиц или на каком-либо другом известном масштабе? Нынешняя тенденция состоит в том, что почти все технические дисциплины (науки) утверждают, что описывают физические проблемы на разных масштабах. Среди множества научных методов, используемых в настоящее время, мы рассматриваем лишь следующие техники как учитывающие разные масштабы: 1) квантовая химия; 2) ФТП (функциональная теория плотности); 3) физическая химия; 4) моделирование в молекулярной динамике (МД); 5) метод огрубленного осреднения; 6) многомасштабные и многофазные методы в клеточной биологии. В общем, эти области должны предусматривать несколько пространственных и временных масштабов, физических моделей, которые могут соответствовать друг другу на стыке смежных масштабных пространств. Методика переноса по масштабам была введена несколько лет назад в качестве способа определения средств и процедур для прямого и строгого «преобразования» данных или модели на одном масштабе к данным на соседнем верхнем или нижнем масштабе. Эти связи между масштабами, масштабные преобразования данных происходят в основном не посредством формул, а чаще всего с помощью масштабных управляющих уравнений для данных явлений. В данном обзоре мы учитываем одномасштабные особенности вышеупомянутых теорий, методов и их потенциала для переноса по масштабам на соседних уровнях.

Ключевые слова: биополимеры, органические полимеры, биовещества, клеточная биология, гетерогенный, многомасштабный, полимасштабный, биологическое моделирование, многомасштабное моделирование, огрубленное осреднение, физическая модель, теорема Гаусса-Остроградского, теории осреднения, теорема WSAM, перенос по масштабам.

QUANTUM CHEMISTRY, PHYSICAL CHEMISTRY, MOLECULAR DYNAMICS SIMULATION, DFT (DENSITY FUNCTIONAL THEORY), AND COARSE-GRAINING TECHNIQUES APPLIED IN STRUCTURAL, CELLULAR BIOLOGY, POLYMER SCIENCE AND IMPLICATION FOR SCALEPORTATION

V.S. Travkin1, N.N. Bolotina1'2

'Hierarchical Scaled Physics and Technologies (HSPT), Los Angeles, CA, USA E-mail: travkin@travkin-hspt.com 2University of Applied Sciences, Rheinbach, Germany

Referred: 15.03.11 Expertise: 23.03.11 Accepted: 25.03.11

There is no substance of physical volumetric content in our known universe that is not a heterogeneous one. The thing is to determine at which scale it becomes as that, at the atomic, planetary, stellar, sub-particle, or other known scale? The current trend is that almost all technical fields can be characterized by attention and claims to the physically multiscale description of problems. Among many scientific techniques used nowadays we consider the following as scale depending: 1) Quantum Chemistry; 2) Density Functional Theory (DFT); 3) Physical Chemistry; 4) Molecular Dynamics (MD) Simulation; 5) Coarse-Graining

International Scientific Journal for Alternative Energy and Ecology № 2 (94) 2011

© Scientific Technical Centre «TATA», 2011

Techniques; 6) Polyscale Polyphase Needs for Cellular Biology. Totally, these fields must provide for the ladder of spatial and temporal scales, physical models that could match one another at the interface between the neighboring scale fields. Scaleportation was introduced some years ago as a definition for the means and procedures of the direct and strict "transformation" of data, model at one scale to the data of the neighboring Upper or Lower Scale. These interscale communications, scale transformations of data are mainly not by formulae, but most often using the scaled governing equations for the phenomena. In this review, we take into consideration one scale features of the above mentioned theories, methods and their potentials for the scaleportation to the neighboring scales.

Keywords: Biopolymer; Organic polymers; Biomedia; Cellular biology; Heterogeneous; Multiscale; Polyscale; Biology modeling; Multiscale modeling; Coarse-Graining; Physical model; Gauss-Ostrogradsky theorem; WSAM theorem; Averaging theories; Scaleportation.

Introduction

1. Some definitions of scaling related to the subject of sub-continuum and continuum physics and modeling of biopolymers, biomedia as scaled media

There is a great need for creation or explanation of biological components, biomedia properties. The current trend is that almost all technical fields can be characterized by attention and claims to the physically multiscale description of problems. Among many scientific techniques used nowadays we consider the following as scale depending or becoming used for scaling studies. We would like to scrutinize the following:

1) Quantum Chemistry;

2) Density Functional Theory (DFT);

3) Physical Chemistry;

4) Molecular Dynamics Simulation;

5) Coarse-Graining Techniques;

6) Polyscale Polyphase Needs for Cellular Biology, Biophysics, etc.

Totally, these fields are thought to be able to provide for the ladder of spatial and temporal scales, physical models that could match one another at the interface between the neighboring scales fields. In reality it is a long way before meeting this goal. At the same time we will be dealing with the problems of multiscale, heterogeneous, nonlocal and nonlinear character that are discussed now in printed literature. We should be concerned about the drawbacks within the techniques themselves along with the proper, correct communication of the different scale fields. Having this in mind, we shall try to maintain a balance between the methods employed at this time while demonstrating what arrays of possibilities can be explored in the future studies.

In each technique mentioned above there has been developed through the periods from their conceptions a number of assumptions and adjustments that are so convenient in use that workers consider them as laws, nevertheless now they must be challenged while making improvements to these techniques; and an upgrade or a change of the physical model will follow.

Most of these improvements can be referred to the proper, stricter treatment of collective, interactive phenomena while taking heterogeneous matters for study. To this kind of phenomena/changes we can relate

almost any action or process more complicated than collision of "mathematical" ball onto the "mathematical" wall, or movement and collisions of two "mathematical" balls, meaning particles, atoms or molecules in MD.

In all other nature prescribed cases the physical matters are of scaled or multiscale character by existence. There is no substance of physical content in our known universe that is not a heterogeneous one.

The question is at what scale down the matter is still homogeneous? That answer we don't know yet. And taking the scale an Upper or Lower one, then we will have the Heterogeneous matter anyway. The volume of the earth can be considered as homogeneous at the galaxy mean scale, meanwhile for our human experiences the earth scale is a huge heterogeneous object. Another sample - water which we can obviously consider as a homogeneous matter? While it is not, at an atomic and lower scales. As always, we need taking into account these physical characteristics of matter description that always hold and are promoted for future quality improvements, and sometimes for quality change. For the better one, of course.

Also, there is no action or process that we can name a local one, unless we want to. Otherwise, we have to look into the point and what it means more strictly. Obviously, many actions or processes can be separated from their less important, at the moment or case, surroundings or/and forces. But that is always more or less an artificial choice. Also we don't know yet - what is or is not the collective influence of the Lower Scale forces, because up to now physicists have been connecting the scales by approximations with the help of appropriate coefficients. We want the issues to be open for the inquiries and we ourselves have the right to inquire.

In these notes we won't be concerned with the multiscale, heterogeneous, nonlocal and nonlinear properties related to scales that are smaller, than what is allegedly used here as of the atomic scales group -(10-11 - 10-10)m. We leave it for the future texts. We would look at the works and critically analyze the molecular to ^ continuum (10-3 - 10-2)m range of scales and techniques used to tackle the intra- and interscale transport tasks of physical nature.

In these -8 orders of decimal magnitude the mentioned physical theories provide mostly for the approximate or even ad-hoc adjusting mechanisms for the two-scale

Международный научный журнал «Альтернативная энергетика и экология» № 2 (94) 2011 © Научно-технический центр «TATA», 2011

Bottom-Up scale communication, and that mode is to be reentered in the current review from the Bottom-Up and Top-Down interscale transport (communications) point of view. This says that the connections of the scale inherited fields are of great significance/importance. The reviewed here studies often have as results of their task solutions

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