arXiv subjects

Adam Gadomski

Publications and source records attributed to Adam Gadomski.

7 recordsLinked to original sources

arXiv2022

Statistical method for analysis of interactions between chosen protein and chondroitin sulfate in an aqueous environment

We present the statistical method to study the interaction between a chosen protein and another molecule (e.g., both being components of lubricin found in synovial fluid) in a water environment. The research is performed on the example of univariate time series of chosen features of the dynamics of mucin, which interact with chondroitin sulfate (4 and 6) in four different saline solutions. Our statistical approach is based on recurrence methods to analyze chosen features of molecular dynamics. Such recurrence methods are usually applied to reconstruct the evolution of a molecular system in its reduced phase space, where the most important variables in the process are taken into account. In detail, the analyzed time-series are spitted onto sub-series of records that are expected to carry meaningful information about the system of molecules. Elements of sub-series are splinted by the constant delay-time lag (that is the parameter determined by statistical testing in our case), and the length of sub-series is the embedded dimension parameter (using the Cao method). We use the recurrent plots approach combined with the Shannon entropy approach to analyze the robustness of the sub-series determination. We hypothesize that the robustness of the sub-series determines some specifics of the dynamics of the system of molecules. We analyze rather highly noised features to demonstrate that such features lead to recurrence plots that graphically look similar. From the recurrence plots, the Shannon entropy has been computed. We have, however, demonstrated that the Shannon entropy value is highly dependent on the delay time value for analyzed features. Hence, elaboration of a more precise method of the recurrence plot analysis is required. For this reason, we suggest the random walk method that can be applied to analyze the recurrence plots automatically.

physics.chem-ph↗

arXiv2018

A tribute to Marian Smoluchowski's legacy on soft grains assembly and hydrogel formation

The paper compares the statistical description of physical-metallurgical processes and ceramic-polycrystalline evolutions, termed the normal grain growth (NGG), as adopted to soft- and chemically-reactive grains, with a Smoluchowski's population-constant kernel cluster-cluster aggregation (CCA) model, concerning irreversible chemical reaction kinetics. The former aiming at comprehending, in a semi-quantitative way, the volume-conservative (pressure-drifted) grain-growth process which we propose to adopt for hydrogel systems at quite low temperature (near a gel point). It has been noticed, that by identifying the mean cluster size $ $ from the Smoluchowski CCA description with the mean cluster radius' size $R_D$, from the NGG approach of proximate grains, one is able to embark on equivalence of both frameworks, but only under certain conditions. For great enough, close-packed clusters, the equivalence can be obtained by rearranging the time domain with rescaled time variable, where the scaling function originates from the dispersive (long-tail, or fractal) kinetics, with a single exponent equal to $d+1$ (in $d$-dimensional (Euclidean) space). This can be of interest for experimenters, working in the field of thermoresponsive gels formation, where crystalline structural predispositions overwhelm.

cond-mat.soft↗

arXiv2017

On Dynamical Systems Theory in Quantitative Psychology and Cognition Science: A Fair Discrimination Between Deterministic and Statistical Counterparts Is Required

The present communication addresses a set of observations, obeying both deterministic as well as statistical formal requirements, and serving to operate within the framework of the dynamical systems theory, with a certain emphasis placed on initial data. It is argued that statistical approaches can manifest themselves non unequivocally, leading to certain virtual discrepancies in psychological and/or cognitive data analyses, termed sometimes in literature as, questionable research practices. This communication points to the demand for a deep awareness of the data origins, which can indicate whether the exponential (Malthus type) or the algebraic (Pareto type) statistical distribution ought to be effectively considered in practical interpretation. This is also related to the question of how frequently patients behave in a specific way, and the significance of these behaviors in determining a patient's progression or regression, involving a certain memory effect. In this perspective, it is discussed how a sensitively applied hazardous or triggering factor can be helpful for well-controlled psychological strategic treatments, also those attributable to obsessive/compulsive disorders or even self-injurious behaviors, with their both criticality and complexity exploiting relations between a therapist and a patient.

physics.soc-ph↗

arXiv2014

Primacy & Ranking of UEFA Soccer Teams from Biasing Organizing Rules

A question is raised on whether some implied regularity or structure, as found in soccer team ranking by the Union of European Football Associations (UEFA), is due to implicit game result value or score competition conditions. The analysis is based on considerations about complex systems, i.e. searching whether power or other simple law fits are appropriate to describe some internal dynamics. It is observed that the ranking is specifically organized: a major class made of a few teams emerges after each game season. Other classes which apparently have regular sizes subsequently occur. Thus, the notion of Sheppard primacy index is envisaged to describe the findings. Additional primacy indices are discussed for enhancing the features. These measures can be used to sort out peer classes in more general terms. A very simplified toy model containing ingredients of the UEFA ranking rules suggests that such peer classes are an extrinsic property of the ranking, as obtained in many nonlinear systems under boundary condition constraints.

physics.soc-ph↗

arXiv2014

Ranking structures and Rank-Rank Correlations of Countries. The FIFA and UEFA cases

Ranking of agents competing with each other in complex systems may lead to paradoxes according to the pre-chosen different measures. A discussion is presented on such rank-rank, similar or not, correlations based on the case of European countries ranked by UEFA and FIFA from different soccer competitions. The first question to be answered is whether an empirical and simple law is obtained for such (self-) organizations of complex sociological systems with such different measuring schemes. It is found that the power law form is not the best description contrary to many modern expectations. The stretched exponential is much more adequate. Moreover, it is found that the measuring rules lead to some inner structures, in both cases.

physics.soc-ph↗

arXiv2011

Controlling protein crystal growth rate by means of temperature

We have proposed a model to analyze the growth kinetics of lysozyme crystals/aggregates under non-isothermal conditions. The model was formulated through an analysis of the entropy production of the growth process which was obtained by taking into account the explicit dependence of the free energy on the temperature. We found that the growth process is coupled with temperature variations resulting in a novel Soret-type effect. We identified the surface entropy of the crystal/aggregate as a decisive ingredient controlling the behavior of the average growth rate as a function of temperature. The behavior of the Gibbs free energy as a function of temperature is also analyzed. The agreement between theory and experiments is very good in the range of temperatures considered.

cond-mat.mtrl-sci↗

arXiv2004

Agglomeration/aggregation and chaotic behaviour in d-dimensional spatio-temporal matter rearrangements. Number-theoretic aspects

Matter gets organized at several levels of structural rearrangements. At mesoscopic level one can distinguish between two types of rearrangements, conforming to different close-packing or densification conditions, appearing during different evolution stages. The cluster formations appear to be temperature- and space-dimension dependent. They suffer a type of Verhulst-like saturation (frustration) when one couples the growing (instability) and mechanical stress relaxation modes together. They manifest a chaotic behavior both in space and time domains. We pretend to offer a comprehensive and realistic picture of a material or megacluster formation in d-dimension.

cond-mat.soft↗