Coarse Graining RNA Nanostructures for Molecular Dynamics Simulations

A series of coarse-grained models have been developed for the study of the molecular dynamics of RNA nanostructures. The models in the series have one to three beads per nucleotide and include different amounts of detailed structural information. Such a treatment allows us to reach, for the systems of thousands of nucleotides, a time scale of microseconds (i.e. by three orders of magnitude longer than in the full atomistic modelling) and thus to enable simulations of large RNA polymers in the context of bionanotechnology. We find that the 3-beads-per-nucleotide models, described by a set of just a few universal parameters, are able to describe different RNA conformations and are comparable in structural precision to the models where detailed values of the backbone P-C4' dihedrals taken from a reference structure are included. These findings are discussed in the context of the RNA conformation classes

Співвідношення можливості та дійсності у правозастосуванні

Палій О. М. Співвідношення можливості та дійсності у правозастосуванні : автореф. дис. ... канд. юрид. наук : 12.00.12 / О. М. Палій; кер. роботи Л. М. Сумарокова; Нац. ун.-т "Одеська юридична академія". – Одеса, 2014. – 16 с.Дисертація на здобуття наукового ступеня кандидата юридичних наук за спеціальністю 12.00.12 – філософія права. – Національний університет «Одеська юридична академія». – Одеса, 2014. У дисертації здійснено комплексне дослідження різних аспектів співвідношення можливості та дійсності у правозастосовній діяльності. В межах проведеного дослідження одержані результати, які мають наукову новизну, зумовлену розв’язанням актуальних проблем у сфері правозастосування, які досі не отримали достатньої розробки у науковій літературі. Загальнометодологічне поняття диспозитивності використовується для аналізу правових норм і процесів правозастосування. Формулюються критерії для вимірювання ступеня здійсненності норм права: співвіднесеність даної норми права з іншими правовими нормами, співвіднесеність норми права з цілями і цінностями суспільства, співвіднесеність з практичними механізмами здійснення права, прийнятність правових приписів для суспільства і сприйняття їх адресатами. Аналізується проблема значимості суб’єктів правозастосування для ефективності правозастосування. Обґрунтовується теза про те, що суб’єкт правозастосування повинен мати всі ознаки дійсної людини у філософському її розумінні, тобто з урахуванням його особистісних якостей.Диссертация на соискание ученой степени кандидата юридических наук по специальности 12.00.12 – философия права. – Национальный университет «Одесская юридическая академия». – Одесса, 2014. В диссертации осуществлено комплексное исследование различных аспектов соотношения возможности и действительности в правоприменительной деятельности. В рамках проведенного исследования получены результаты, имеющие научную новизну, обусловленную решением актуальных проблем в сфере правоприменения, которые не получили достаточной разработки в научной литературе. На основе анализа категорий возможности и действительности как философских категорий, уточнены понятия правовой возможности и правовой действительности. Общеметодологическое понятие диспозитивности модифицируется для контекстов анализа правовых норм и процессов правоприменения. Вводятся понятия диспозитивности норм права, диспозитивности поведения адресатов норм и субъектов правоприменения. Формулируются критерии для измерения степени осуществимости норм права: соотнесенность данной нормы права с другими правовыми нормами (степень связности системы норм), соотнесенность нормы права с действующими целями и ценностями общества (релевантность нормы аксиосфере права и аксиосфере культуры), соотнесенность с практическими механизмами осуществления права (наличие заранее установленного алгоритма практического осуществления возможности), а также приемлемость правовых предписаний для общества, принятие их адресатами. Автор, анализируя дискуссии по поводу структуры правоприменения, отстаивает точку зрения, которая заключается в том, что завершающей стадией процесса правоприменения следует считать осуществление решения специализированного органа, поскольку только после полного восстановления нарушенного или затрудненного правоотношения норму права можно считать примененной, а процесс правоприменения завершенным. Анализируется проблема значимости субъектов правоприменения для эффективности правоприменения. Обосновывается тезис о том, что субъект правоприменения должен обладать всеми признаками действительного человека в философском его понимании, то есть с учетом его профессиональных и личностных качеств. Действительный человек – это единство и полнота всех проявлений его человеческой сущности во всех сферах его бытия: духовной, практической, поведенческой и т.д. Обосновано, что философское образование играет важнейшую роль в процессе подготовки субъекта правоприменения, в его воспитании как целостной личности, то есть «действительного человека». Философское знание помогает человеку в формировании мировоззрения как самосознания и как важного регулятива профессиональной деятельности.The thesis for a Candidate of Law Degree in the Specialty 12.00.12 – Philosophy of Law. – National University «Odessa Law Academy». – Odessa, 2014. The thesis presents a comprehensive study of various aspects of possibility and reality correspondence in the law enforcement. As part of the research the results of the scientific novelty have been got due to the solution of actual problems in the field of the law enforcement which have not received an adequate development in the scientific literature. The optionality general methodological concept is modified to the context of analyzing legal rules and law enforcement processes. The criteria for measuring the law feasibility degree are formulated: the correlation of enforcing legal norm with other legal norms, the correlation of the enforcing legal norm with the goals and values of the society, correlation with the practical implementation of the legal mechanisms and the acceptability of legal norms for the society and their clearness for the addressees. The problem of the subjects of the law enforcement significance for the law enforcement effectivity is analyzed. The thesis that the law enforcement subject should have all the characteristics of a real person in his philosophical sense, taking into account his personal qualities, is justified

Driven Dynamics: A Probable Photodriven Frenkel-Kontorova Model

In this study, we examine the dynamics of a one-dimensional Frenkel-Kontorova chain consisting of nanosize clusters (the ''particles'') and photochromic molecules (the ''bonds''), and being subjected to a periodic substrate potential. Whether the whole chain should be running or be locked depends on both the frequency and the wavelength of the light (keeping the other parameters fixed), as observed through numerical simulation. In the locked state, the particles are bound at the bottom of the external potential and vibrate backwards and forwards at a constant amplitude. In the running state, the initially fed energy is transformed into directed motion as a whole. It is of interest to note that the driving energy is introduced to the system by the irradiation of light, and the driven mechanism is based on the dynamical competition between the inherent lengths of the moving object (the chain) and the supporting carrier (the isotropic surface). However, the most important is that the light-induced conformational changes of the chromophore lead to the time-and-space dependence of the rest lengths of the bonds.Comment: 4 pages,5 figure

Dynamical transitions in correlated driven diffusion in a periodic potential

The diffusion of a two-dimensional array of particles driven by a constant force in the presence of a periodic external potential exhibits a hierarchy of dynamical phase transitions when the driving force is varied. This behavior can be explained by a simple phenomenological approach which reduces the system of strongly interacting particles to weakly interacting quasi-particles (kinks). The richness of the strongly coupled system is however not lost because, contrary to a single-Brownian particle, the array shows an hysteretic behavior even at non-zero temperature. The present investigation can be viewed as a first step toward understanding nanotribology.Comment: 4 pages, 3 pictures, revtex to appear in Phys Rev. Let

On the driven Frenkel-Kontorova model: II. Chaotic sliding and nonequilibrium melting and freezing

The dynamical behavior of a weakly damped harmonic chain in a spatially periodic potential (Frenkel-Kontorova model) under the subject of an external force is investigated. We show that the chain can be in a spatio-temporally chaotic state called fluid-sliding state. This is proven by calculating correlation functions and Lyapunov spectra. An effective temperature is attributed to the fluid-sliding state. Even though the velocity fluctuations are Gaussian distributed, the fluid-sliding state is clearly not in equilibrium because the equipartition theorem is violated. We also study the transition between frozen states (stationary solutions) and=7F molten states (fluid-sliding states). The transition is similar to a first-order phase transition, and it shows hysteresis. The depinning-pinning transition (freezing) is a nucleation process. The frozen state contains usually two domains of different particle densities. The pinning-depinning transition (melting) is caused by saddle-node bifurcations of the stationary states. It depends on the history. Melting is accompanied by precursors, called micro-slips, which reconfigurate the chain locally. Even though we investigate the dynamics at zero temperature, the behavior of the Frenkel-Kontorova model is qualitatively similar to the behavior of similar models at nonzero temperature.Comment: Written in RevTeX, 13 figures in PostScript, appears in PR

Parallel updating cellular automaton models of driven diffusive Frenkel-Kontorova-type systems

Three cellular automaton (CA) models of increasing complexity are introduced to model driven diffusive systems related to the generalized Frenkel-Kontorova (FK) models recently proposed by Braun [Phys.Rev.E58, 1311 (1998)]. The models are defined in terms of parallel updating rules. Simulation results are presented for these models. The features are qualitatively similar to those models defined previously in terms of sequentially updating rules. Essential features of the FK model such as phase transitions, jamming due to atoms in the immobile state, and hysteresis in the relationship between the fraction of atoms in the running state and the bias field are captured. Formulating in terms of parallel updating rules has the advantage that the models can be treated analytically by following the time evolution of the occupation on every site of the lattice. Results of this analytical approach are given for the two simpler models. The steady state properties are found by studying the stable fixed points of a closed set of dynamical equations obtained within the approximation of retaining spatial correlations only upto two nearest neighboring sites. Results are found to be in good agreement with numerical data.Comment: 26 pages, 4 eps figure

Dynamical phase diagram of the dc-driven underdamped Frenkel-Kontorova chain

Multistep dynamical phase transition from the locked to the running state of atoms in response to a dc external force is studied by MD simulations of the generalized Frenkel-Kontorova model in the underdamped limit. We show that the hierarchy of transition recently reported [Braun et al, Phys. Rev. Lett. 78, 1295 (1997)] strongly depends on the value of the friction constant. A simple phenomenological explanation for the friction dependence of the various critical forces separating intermediate regimes is given.Comment: 12 Revtex Pages, 4 EPS figure

Stokes' Drift of linear Defects

A linear defect, viz. an elastic string, diffusing on a planar substrate traversed by a travelling wave experiences a drag known as Stokes' drift. In the limit of an infinitely long string, such a mechanism is shown to be characterized by a sharp threshold that depends on the wave parameters, the string damping constant and the substrate temperature. Moreover, the onset of the Stokes' drift is signaled by an excess diffusion of the string center of mass, while the dispersion of the drifting string around its center of mass may grow anomalous.Comment: 14 pages, no figures, to be published in Phys.Rev.

On the driven Frenkel-Kontorova model: I. Uniform sliding states and dynamical domains of different particle densities

The dynamical behavior of a harmonic chain in a spatially periodic potential (Frenkel-Kontorova model, discrete sine-Gordon equation) under the influence of an external force and a velocity proportional damping is investigated. We do this at zero temperature for long chains in a regime where inertia and damping as well as the nearest-neighbor interaction and the potential are of the same order. There are two types of regular sliding states: Uniform sliding states, which are periodic solutions where all particles perform the same motion shifted in time, and nonuniform sliding states, which are quasi-periodic solutions where the system forms patterns of domains of different uniform sliding states. We discuss the properties of this kind of pattern formation and derive equations of motion for the slowly varying average particle density and velocity. To observe these dynamical domains we suggest experiments with a discrete ring of at least fifty Josephson junctions.Comment: Written in RevTeX, 9 figures in PostScrip