Hierarchical Levels Of Organization Research Articles

Navigating Pubertal Goldilocks: The Optimal Pace for Hierarchical Brain Organization.

Adolescence is a timed process with an onset, tempo, and duration. Nevertheless, the temporal dimension, especially the pace of maturation, remains an insufficiently studied aspect of developmental progression. The primary objective is to estimate the precise influence of pubertal maturational tempo on the configuration of associative brain regions. To this end, the connection between maturational stages and the level of hierarchical organization of large-scale brain networks in 12-13-year-old females is analyzed. Skeletal maturity is used as a proxy for pubertal progress. The degree of maturity is defined by the difference between bone age and chronological age. To assess the level of hierarchical organization in the brain, the temporal dynamic of closed eye resting state high-density electroencephalography (EEG) in the alpha frequency range is analyzed. Different levels of hierarchical order are captured by the measured asymmetry in the directionality of information flow between different regions. The calculated EEG-based entropy production of participant groups is then compared with accelerated, average, and decelerated maturity. Results indicate that an average maturational trajectory optimally aligns with cerebral hierarchical order, and both accelerated and decelerated timelines result in diminished cortical organization. This suggests that a "Goldilocks rule" of brain development is favoring a particular maturational tempo.

Interactive effects of intrinsic and extrinsic factors on metabolic rate.

Metabolism energizes all biological processes, and its tempo may importantly influence the ecological success and evolutionary fitness of organisms. Therefore, understanding the broad variation in metabolic rate that exists across the living world is a fundamental challenge in biology. To further the development of a more reliable and holistic picture of the causes of this variation, we review several examples of how various intrinsic (biological) and extrinsic (environmental) factors (including body size, cell size, activity level, temperature, predation and other diverse genetic, cellular, morphological, physiological, behavioural and ecological influences) can interactively affect metabolic rate in synergistic or antagonistic ways. Most of the interactive effects that have been documented involve body size, temperature or both, but future research may reveal additional 'hub factors'. Our review highlights the complex, intimate inter-relationships between physiology and ecology, knowledge of which can shed light on various problems in both disciplines, including variation in physiological adaptations, life histories, ecological niches and various organism-environment interactions in ecosystems. We also discuss theoretical and practical implications of interactive effects on metabolic rate and provide suggestions for future research, including holistic system analyses at various hierarchical levels of organization that focus on interactive proximate (functional) and ultimate (evolutionary) causal networks. This article is part of the theme issue 'The evolutionary significance of variation in metabolic rates'.

Identification and characterization of unknown disturbances in a structured population using high-throughput phenotyping data and measurement of robustness: application to growing pigs.

Improving the robustness of animals has become a priority in breeding due to climate change, new societal demands, and the agroecological transition. Components of animal robustness can be extracted from the analysis of the adaptive response of an animal to disturbance using longitudinal data. Nonetheless, this response is a function of animal robustness as well as of disturbance characteristics (intensity and duration). To correctly assess an animal's robustness potential, it is therefore useful to know the characteristics of the disturbances it faces. The UpDown method, which detects and characterizes unknown disturbances at different levels of organization of the population (e.g., individual, pen, and batch disturbances), has been proposed for this purpose. Furthermore, using the outputs of the method, it is possible to extract proxies of the robustness of animals. In this context, the objective of the study was to evaluate the performances of the UpDown method to detect and characterize disturbances and quantify the robustness of animals in a genetic framework using different sets of simulations, and to apply this method to real pig longitudinal data recorded during the fattening period (body weight, cumulative feed intake, and feeding rate). Based on the simulations, the specificity of the UpDown method was high (>0.95). Its sensitivity increased with the level of organization exposed (from 0.23 to 0.32 for individual disturbances, from 0.45 to 0.59 for pen disturbances, and from 0.77 to 0.88 for batch disturbances). The UpDown method also showed a good ability to characterize detected disturbances. The average time interval between the estimated and true start date or duration of the disturbance was lower than 3d. The correlation between the true and estimated intensity of the disturbance increased with the hierarchical level of organization (on average, 0.41, 0.78, and 0.83 for individual, pen, and batch disturbance, respectively). The accuracy of the estimated breeding values of the proxies for robustness extracted from the analysis of individual trajectories over time were moderate (lower than 0.33). Applied to real data, the UpDown method detected different disturbances depending on the phenotype analyzed. The heritability of the proxies of robustness were low to moderate (ranging from 0.11 to 0.20).

Effects of environmental translocation and host characteristics on skin microbiomes of sun-basking fish.

Variation in the composition of skin-associated microbiomes has been attributed to host species, geographical location and habitat, but the role of intraspecific phenotypic variation among host individuals remains elusive. We explored if and how host environment and different phenotypic traits were associated with microbiome composition. We conducted repeated sampling of dorsal and ventral skin microbiomes of carp individuals (Cyprinus carpio) before and after translocation from laboratory conditions to a semi-natural environment. Both alpha and beta diversity of skin-associated microbiomes increased substantially within and among individuals following translocation, particularly on dorsal body sites. The variation in microbiome composition among hosts was significantly associated with body site, sun-basking, habitat switch and growth, but not temperature gain while basking, sex, personality nor colour morph. We suggest that the overall increase in the alpha and beta diversity estimates among hosts were induced by individuals expressing greater variation in behaviours and thus exposure to potential colonizers in the pond environment compared with the laboratory. Our results exemplify how biological diversity at one level of organization (phenotypic variation among and within fish host individuals) together with the external environment impacts biological diversity at a higher hierarchical level of organization (richness and composition of fish-associated microbial communities).

Diversity–functioning relationships across hierarchies of biological organization

Numerous biodiversity–ecosystem functioning (BEF) experiments have shown that plant community productivity typically increases with species diversity. In these studies, diversity is generally quantified using metrics of taxonomic, phylogenetic, or functional differences among community members. Research has also shown that the relationships between species diversity and functioning depends on the spatial scale considered, primarily because larger areas may contain different ecosystem types and span gradients in environmental conditions, which result in a turnover of the species set present locally. A fact that has received little attention, however, is that ecological systems are hierarchically structured, from genes to individuals to communities to entire landscapes, and that additional biological variation occurs at levels of organization above and below those typically considered in BEF research. Here, we present cases of diversity effects at different hierarchical levels of organization and compare these to the species‐diversity effects traditionally studied. We argue that when this evidence is combined across levels, a general framework emerges that allows the transfer of insights and concepts between traditionally disparate disciplines. Such a framework presents an important step towards a better understanding of the functional importance of diversity in complex, real‐world systems.

Definitions of parasitism, considering its potentially opposing effects at different levels of hierarchical organization.

An annotated synthesis of textbook definitions of parasitism is presented. Most definitions declare parasitism is a long-lasting relationship between individuals of different species harming the hosts. The infection-induced costs are interpreted as diseases in the medical-veterinary literature. Alternatively, evolutionary ecologists interpret it as a reduction of host's fitness (longevity, fertility or both). Authors often assume that such effects decrease host population growth and select for antiparasitic defences, which is not necessarily true because infections may simultaneously express opposite effects at different levels of biological organization. (i) At the cellular level, infection-induced cell growth, longevity and multiplication may yield tumours maladaptive at higher levels. (ii) At the individual level, reduced host longevity, fertility or both are interpreted as disease symptoms or reduced fitness. (iii) Contrary to common sense, the growth rate of infected host lineages may increase in parallel with the individuals' reduced survival and fertility. This is because selection favours not only the production of more offspring but also their faster production. (iv) Finally, infections that reduce host individuals' or lineages' fitness may still increase infected host populations' growth rate in the context of ecological competition. Therefore, differences between parasitism and mutualism may depend on which level of organization one focuses on.

Assembly of a Diphenylalanine Peptide Nanotube by Molecular Dynamics Methods

The paper develops an approach to modeling the processes of self-assembly of complex molecular nanostructures by molecular dynamics methods using a molecular dynamics manipulator. Previously, this approach was considered using the example of assembling a phenylalanine helical nanotube from a linear set of chains of phenylalanine (F) molecules of different chirality: left-handed L-F and right-handed D-F chirality L-FF and D-FF. The process of self-assembly of dipeptide chains into helical structures of nanotubes is an imitation of applying certain forces to the existing initial linear structure in order to obtain the final structure of the same chemical composition, but with a different helical geometry. The PUMA-CUDA molecular dynamics simulation software package was used as the main software. Using this tool, one can investigate the formation of helical structures from a linear sequence of any amino acids. A comparative analysis of the structures of nanotubes obtained by assembling by molecular dynamics methods and by their experimental self-assembly was performed using the method of visual differential analysis. It has been established that the obtained data correspond to the law of the sign change of chirality of molecular helical structures with the complication of their hierarchical level of organization.

Methodological scheme of qualimetric assessment of recreational clusters


 
 
 The article deals with the application of qualimetric methods for assessing recreational and tourist potential on the example of an ecotourism cluster developed for natural and geographical and socio-economic conditions and resources of the Ukrainian Black Sea region. The properties of recreational and tourist potential can have different nature, different definitions, and be qualitative-descriptive, verbal, or quantitative (numerical). In qualimetric developments, properties should be comparable in the form of representation and magnitude of evaluation scales. The aim of the study is to develop a methodology for qualimetric assessment of recreational clusters. The theoretical and methodological basis is the fundamental principles and developments of recreational geography, tourism studies and qualimetry, as well as the author’s own developments. In the process of writing, general geographical methods were used, such as descriptive, comparative geographical, and qualimetric assessment methods. Characteristics and properties presented in verbal form can be shown as structural combinations and compounds of simpler indicators. Factors that form the recreational and tourist potential have different weights (significance), which requires an appropriate assessment. The overall assessment of recreational and tourist potential is a weighted average value of all its components, taking into account their weight. The available absolute natural indicators of conditions and resources of recreational and tourist potential are also transformed into qualimetric estimates. The general methodological scheme for assessing recreational clusters, specified according to the conditions and resources of ecotourism of the Black Sea region is represented by seven stages – from structuring a recreational cluster according to its components and levels of hierarchical organization, calculating indicators of the weight of properties and calculating criteria for prop- erties that form the corresponding quality, calculating qualimetric estimates for all primary units of recreational and tourist potential; a meaningful interpretation of the assessment of the recreational and tourist potential of a recreational cluster based on the criteria of properties and scales of the corresponding features and characteristics, as well as indicators of the weight of properties in the formation of recreational and tourist potential. The developed scheme should be considered as a methodological approach for the practical application of qualimetric assessments of recreational and tourist potential in recreational geography and tourism studies.
 
 

Intra-individual variation in Galium odoratum is affected by experimental drought and shading.

Climate-change induced warmer spring temperatures advance tree leaf-out and result in earlier shading of the forest floor. Climate change also leads to more frequent droughts. Forest understorey herbs may respond to these environmental changes by varying traits at different hierarchical levels of organization. While trait mean variation at the inter-individual level in response to environmental changes is well-studied, little is known about how variation at the intra-individual level responds. We sampled genets of the forest understorey herb Galium odoratum from 21 populations in three regions in Germany, varying in microclimatic conditions. The genets were transplanted into a common garden, where we applied shading and drought treatments. We measured plant height and leaf length and width, and calculated the coefficient of variation (CV) at different hierarchical levels: intra-population, intra-genet, intra-ramet and intra-shoot. Variance partitioning showed that intra-shoot CV represented most of the total variation, followed by intra-ramet CV. We found significant variation in CV of plant height and leaf width among populations of origin, indicating that CV is at least partly genetically based. The soil temperature at populations' origins correlated negatively with CV in plant height, suggesting adaptation to local conditions. Furthermore, we observed that early shade led to increased intra-ramet CV in leaf length, while drought reduced intra-shoot CV in leaf width. Finally, intra-shoot leaf width mean and CV were independent under control conditions but correlated under drought. Our experimental results reveal correlations of intra-individual variation with soil temperature, indicating that intra-individual variation can evolve and may be adaptive. Intra-individual variation responded plastically to drought and shading, suggesting functional changes to improve light capture and reduce evapotranspiration. In conclusion, intra-individual variation makes up the majority of total trait variation in this species and can play a key role in plant adaptation to climatic change.

Часова динаміка морфометричних характеристик фітопланктону в прибережній акваторії Криму (Чорне море, Україна)

The morphometric characteristics of algae at different levels of hierarchical organization – cells, species, functional complexes of species, taxa (diatom algae, dinoflagellates) and phytoplankton as a whole were analyze. Study based on the results of monitoring carried out near the shores of Sevastopol (the Black Sea) in different periods (2004−2006 and 2009−2014), using the cells shape sphericity index (CSSI). It is shown that for each period there is a certain range of fluctuations of average values, both in seasonal and interannual dynamics. A comparison of the two investigated periods by the average CSSI showed a statistically significant decrease in diatoms and a slight increase in dinoflagellates, which may be associated with a shift in the species composition of diatom algae towards more elongated forms, and more rounded in dinoflagellates. Based on the example of two species with elongated cell forms: the diatom Proboscia alata (Brightwell) Sundström and the dinoflagellate Tripos furca (Ehrenberg) F.Gómez, as well as on the 3rd complex as a whole, a significant positive correlation with the water density on the surface was found with the 99% confidence level, which quantitatively confirms their seasonal polymorphism. The analysis of the seasonal dynamics of CSSI of diatoms as a whole showed statistically significant differences and a wide range of fluctuations by month. In the seasonal dynamics, three waves with an interval of four months were found, which corresponded to the seasonal course of the population quantity, except for the March bloom of the 2nd complex representatives belonging to the genus Pseudo-nitszchia H.Peragallo, as a result of which the CSSI was minimal. The May and September maxima of numbers corresponded to the maxima of the CSSI due to bloom and the development of the 1st complex representatives, mainly of the genus Chaetoceros Ehrenberg. For dinoflagellates seasonal differences were not significant and varied within a narrow range, with high mean values (above 0.94) for most of the year. The CSSI minima coincided with the population maxima in May and October. The range of CSSI fluctuations in the seasonal dynamics of diatoms (34.7%) was an order of magnitude higher than that of dinoflagellates (3.7%), which indicates a more stable grouping structure of the latter. Therefore, the average form depends to a large extent on species diversity. At the same time, diatoms are characterized by greater plasticity in adapting to environmental conditions. All phytoplankton are characterized by high CSSI values for most of the year due to the predominance of small flagellates and Prymnesiophyceae algae, with an episodic decrease during the period of diatom bloom in spring and autumn. The rounding of the grouping of both diatoms and dinoflagellates in 2010 May be a response to an abnormally high temperature of water, which led to the intensification of trophic processes in the marine environment. The obtained results can be used as a baseline for comparison in case of resumption of monitoring in this area in the future. The proposed method can be used as a basis for carrying out similar monitoring in any other water area of any type of reservoir.

Problems and prospects of the territorial development of the tourism system in the Almaty region

Introduction: The tourism sector is recognized as an important sector of the economy of the Republic of Kazakhstan. As a member state of the UN, Kazakhstan integrates the Sustainable Development Goals (SDGs) into the State program for the development of the tourism industry. The incomplete implementation of the SDGs in Kazakhstan has causes of global and regional level. Materials and Methods: Statistical indicators for tourism in the Republic of Kazakhstan indicate a stable positive dynamics of the tourist flow in the country. The Almaty region has the highest rates of tourism activity, which has favorable historical, cultural and unique natural prerequisites. Results and Discussion: In the general tourist flow of the region, local tourism prevails. The indicator of inbound tourism in the Almaty region as a whole with the largest city of the Republic of Kazakhstan Almaty is the highest in the country. The target state setting for the prospective development of tourism assumes an increase in the share of tourism in the total GDP of the Republic of Kazakhstan by 2025 by 33%. Conclusions: In the study, in accordance with the concept of territorial and functional development of tourism and recreation in the Republic of Kazakhstan and the terminology of the urban planning direction, three key hierarchical levels of organization of tourist and recreational entities were formulated: regional, district, local – “tourist and recreational region”, “recreational agglomeration”, “tourist and recreational area”. The regional level corresponds to the Almaty tourist and recreational region, the recreational agglomeration - Taldykorgan and Almaty tourist and recreational agglomerations. Within the boundaries of the region, five tourist and recreational areas have been identified.

Questioning Consilience and Autonomy in Self‐Determination Theory: A Critique and Hermeneutic‐Phenomenological Alternative

AbstractThis paper offers a theoretical analysis of Self‐Determination Theory (SDT) and its claims regarding human autonomy. Self‐determination theorists have advanced a form of self‐regulated, engaged behavior (i.e., autonomy), founded upon on a consilient account of human motivation that assumes multiple, hierarchical levels of organization and causation (e.g., biological, psychological, and social). Autonomy, from this perspective, is taken to emerge from underlying biological mechanisms, but also able to exert its own causal effects in the world as a unique psychological phenomenon. We contend that in theorizing this way, self‐determination theorists have invoked a mixed discourse of mechanism and autonomy that leaves important questions unanswered, perhaps most importantly those concerning how autonomy as a kind of volition can fit coherently in the mechanistic account of world that they advocate. We then offer an alternative perspective based upon the work of various hermeneutic‐phenomenological thinkers in philosophy and psychology. This alternative perspective conceptualizes human phenomena such as autonomy and motivation in agentic terms, emphasizing meaningful participation in possibility‐laden contexts of everyday practices.

Stability and asynchrony of local communities but less so diversity increase regional stability of Inner Mongolian grassland.

Extending knowledge on ecosystem stability to larger spatial scales is urgently needed because present local-scale studies are generally ineffective in guiding management and conservation decisions of an entire region with diverse plant communities. We investigated stability of plant productivity across spatial scales and hierarchical levels of organization and analyzed impacts of dominant species, species diversity, and climatic factors using a multisite survey of Inner Mongolian grassland. We found that regional stability across distant local communities was related to stability and asynchrony of local communities. Using only dominant instead of all-species dynamics explained regional stability almost equally well. The diversity of all or only dominant species had comparatively weak effects on stability and synchrony, whereas a lower mean and higher variation of precipitation destabilized regional and local communities by reducing population stability and synchronizing species dynamics. We demonstrate that, for semi-arid temperate grassland with highly uneven species abundances, the stability of regional communities is increased by stability and asynchrony of local communities and these are more affected by climate rather than species diversity. Reduced amounts and increased variation of precipitation in the future may compromise the sustainable provision of ecosystem services to human well-being in this region.

Soil degradation kinetics of oxybenzone (Benzophenone-3) and toxicopathological assessment in the earthworm, Eisenia fetida

A preponderance of recent evidence indicates that oxybenzone and other personal-care product chemicals threaten the biota inhabiting various ecological niches. What is understudied is the ecotoxicological impact of oxybenzone, a UV filter in sunscreens and anti-aging products, to terrestrial/soil organisms that are keystone species in these habitats. In the present study, acute exposure (14-day) to oxybenzone resulted in earthworm mortality (LC50 of 364 mg/kg) and growth rate inhibition. Environmentally relevant concentration of oxybenzone (3.64, 7.28 and 36.4 mg/kg) at exposures of 7-day, 14-day, 28-day induced oxidative stress and neurotoxicity followed by perturbations in reproduction processes and changes in vital organs. Decreased levels of superoxide dismutase (SOD) and catalase (CAT) activity were statistically lower than controls (p < 0.05) on day 14 for all three concentrations, while glutathione-s-transferase (GST) activity was significantly elevated from controls on days 7 and 14. On day 28, SOD and CAT activities were either not significantly different from the control or were higher, demonstrating a temporal multiphasic response of anti-oxidant enzymes. GST activity on day 28 was significantly reduced compared to controls. Acetylcholinesterase levels across the three-time points exhibited a complicated behaviour, with every exposure concentration being significantly different from the control. Chronic exposure negatively influences earthworm health status with elevated biomarker values analysed using IBRv2 index. This, in turn, impacted higher levels of hierarchical organization, significantly impairing reproduction and organismal homeostasis at the histological level and manifesting as decreasing cocoon formation and successful hatching events. Thus, the overall findings demonstrate that oxybenzone is toxic to Eisenia fetida at low-level, long-term exposure. Based on the concentration verification analysis and application of the EPA PestDF tool, oxybenzone undergoes single first-order kinetics degradation in OECD soil with DT50 and DT90 as 8.7–28.9 days, respectively.

Hierarchical heterogeneous one-dimensional problem in linear viscoelastic media

We address the homogenisation of a linear viscoelastic and hierarchical composite material in a one-dimensional (1D) framework via a three-scale asymptotic homogenisation method. We consider a family of heterogeneous problems with periodic, rapidly-oscillating and piece-wise coefficients that model a structure with two hierarchical levels of organisation. Here, we assume continuity contact conditions at the interfaces among the constituents and set a straightforward geometrical configuration in order to gain a better insight of the multiscale problem. The main goal is to provide a general overview of the procedure and validate the approach by means of a comparison between the solution of the original heterogeneous problem, the homogenised problem and the formal asymptotic solution. In addition, we show that the three-scale approach presents a clear improvement over the recursive two-scale one, and we illustrate the convergence of the solutions towards the solution of the homogenised problem when the asymptotic parameters approach.

Non-Covalent Interactions in Organic, Organometallic, and Inorganic Supramolecular Systems Relevant for Medicine, Materials Science, and Catalysis

The structure, fundamental properties, and reactivity of chemical systems at various hierarchical levels of organization of matter is the paradigm of chemistry. A qualitative and quantitative description of various intermolecular and intramolecular non-covalent interactions in chemical systems is the main tool for supramolecular design and the driving force of smart prediction of kinetic and thermodynamic parameters of chemical reactions. This perspective is dedicated to highlighting the recent progress of our research group in the investigation of various non-covalent contacts in organic, organometallic, and inorganic chemical systems relevant for medicine, materials science, and catalysis. This research is interdisciplinary in nature and lies at the intersection of computer modeling with such natural science disciplines as chemistry, physics, crystallography, biology, and medicine, as well as directly related to materials science and nanotechnology.

Modeling of Self-Assembled Peptide Nanotubes and Determination of Their Chirality Sign Based on Dipole Moment Calculations.

The chirality quantification is of great importance in structural biology, where the differences in proteins twisting can provide essentially different physiological effects. However, this aspect of the chirality is still poorly studied for helix-like supramolecular structures. In this work, a method for chirality quantification based on the calculation of scalar triple products of dipole moments is suggested. As a model structure, self-assembled nanotubes of diphenylalanine (FF) made of L- and D-enantiomers were considered. The dipole moments of FF molecules were calculated using semi-empirical quantum-chemical method PM3 and the Amber force field method. The obtained results do not depend on the used simulation and calculation method, and show that the D-FF nanotubes are twisted tighter than L-FF. Moreover, the type of chirality of the helix-like nanotube is opposite to that of the initial individual molecule that is in line with the chirality alternation rule general for different levels of hierarchical organization of molecular systems. The proposed method can be applied to study other helix-like supramolecular structures.

Reduction, reorganization and stasis in the evolution of turtle shell elements

Abstract Novel phenotypic configurations can profoundly alter the evolutionary trajectories of species. Although innovation can precede lengthy periods of evolutionary stasis, the potential for species to diversify further can be realized via modular changes across distinct levels of hierarchical organization. To test this expectation, we undertook anatomical network analyses to model the organization and composition of the turtle’s shell. Our results suggest that stem turtles featured the greatest diversity in the number of skeletal (bones) and epidermal (scutes) shell elements. The shell subsequently underwent numerical simplification. Thus, the sum of potential connections (links) in shell networks has diminished in modern turtles. Some network system descriptors of complexity, integration and modularity covaried with the number of network components (nodes), which has remained evolutionarily stable since the Jurassic. We also demonstrated that shell reorganization might be feasible within modular subdivisions, particularly in modern turtles with simplified and less integrated network structures. We discuss how these findings align with previous studies on numerical simplification with enhanced skeletal specialization in the tetrapod skull. Altogether, our analyses expose the evolvability of the turtle’s shell and bolster the foundation for further macroevolutionary comparisons of ancient and modern species.

Rats’ use of hierarchical organization in serial pattern learning

Many organisms show aptitude for learning and performing patterned sequences. However, we do not yet have a complete account of how they accomplish this. One of the most successful is Restle’s hierarchical model, which supposes organisms represent sequences using the simplest form available through using hierarchies to organize the sequences’ elements. In two experiments, we evaluated if Restle’s model accurately accounted for rats’ patterned sequence learning. First, we compared rats’ learning of a runs pattern with three levels of hierarchical organization with no violations of pattern structure to learning of the same pattern with one violation of pattern structure in the pattern’s second half. Restle’s model predicts rats should have more difficulty learning the violation pattern and that rats learning the pattern with the violation in the second half of the pattern should attempt to reflect that violation to the first half. The results indicated that rats had more difficulty learning the violation pattern and that inserting a violation in the second half of the pattern led rats to make significantly more errors on the second half of the pattern relative to the first half of the pattern. Rats did not insert the violation from the second half of the pattern into the first half of the pattern. In a second experiment, we continued to explore if Restle’s model accurately accounted for rats’ pattern learning using more complex patterns. The present results of both experiments and prior work with humans were inconsistent with Restle’s model, suggesting more work is needed to develop a model that accurately accounts for rats’ learning of complex patterned sequences.

Assembly of a Phenylalanine Nanotube by the use of Molecular Dynamics Manipulator

Studies of the processes of self-organization and self-assembly of various complexly organized (including spiral) structures based on amino acids intensively carried out in recent years. Various methods of molecular modeling, including molecular dynamics (MD) methods, are developed. In this paper, we propose a new approach for a relatively simple technique for conducting MD simulation (MDS) of various molecular nanostructures, determining the trajectory of the MD run and forming the final structure: a molecular dynamic manipulator (MD manipulator). It is an imitation of the operation of an existing or imaginary device or structure by applying force to the existing initial structure in order to obtain a new final structure, having the same chemical composition, but with a different geometry (topology). The PUMA-CUDA software package was applied as the main MD modeling program, which uses the physics of the PUMA software package, developed by the laboratory headed by N.K. Balabaev. Using this MDS tool, you can investigate the formation of helical structures from a linear sequence of any amino acids variation. As an example, the applicability of the developed algorithm for assembling nanotubes from linear phenylalanine (Phe) chains of different chirality (left L-Phe and right D-Phe) is considered by including additional force effects in the molecular dynamics simulation program for these structures. During the MD run, the applied actions, which are the same for the left and right helices of the formed nanotubes, lead the system to an α-helix structure. The work was carried out in an interactive mode using a number of additional programs, incl. trajectory analyzer program MD (TAMD). As a result, the modes that are most adequate for the formation of nanotubes of the right chirality D from the initial L-Phe monomer and nanotubes of the left chirality L from the D-Phe amino acid monomer were determined. The results obtained were compared with data from other works on modeling similar nanotubes of different chirality and experimental data. These are fully in line with the law of change in sign of chirality of molecular structures with complication of their hierarchical level of organization. The molecular animation of the assembly of a left-chiral nanotube from D-monomers is freely available at: http://lmd.impb.ru/Supplementary/PHE.avi.