(Non)Resonance Bonds in Molecular Dynamics Simulations: A Case Study concerning C Fullerenes.

In the case of certain chemical compounds, especially organic ones, electrons can be delocalized between different atoms within the molecule. These resulting bonds, known as resonance bonds, pose a challenge not only in theoretical descriptions of the studied system but also present difficulties in simulating such systems using molecular dynamics methods. In computer simulations of such systems, it is often common practice to use fractional bonds as an averaged value across equivalent structures, known as a resonance hybrid.

Spherulites: How Do They Emerge at an Onset of Nonequilibrium Kinetic-Thermodynamic and Structural Singularity Addressing Conditions?

This communication addresses the question of the far-from-equilibrium growth of spherulites with different growing modes. The growth occurs in defects containing and condensed matter addressing environments of (bio)polymeric and biominerals involving outcomes. It turns out that it is possible to anticipate that, according to our considerations, there is a chance of spherulites' emergence prior to a pure diffusion-controlled (poly)crystal growth.

Hyaluronan-Chondroitin Sulfate Anomalous Crosslinking Due to Temperature Changes.

Glycosaminoglycans are a wide class of biopolymers showing great lubricating properties due to their structure and high affinity to water. Two of them, hyaluronic acid and chondroitin sulfate, play an important role in articular cartilage lubrication. In this work, we present results of the all-atom molecular dynamics simulations of both molecules placed in water-based solution.

Gallstone formation as an example of the two-step space confined aggregation process.

Gallstone disease and in particular its cholesterol type is one of the most common diseases of the digestive system. More than 10% of the population is affected by this disease and in the case of Native Indians of Peru and Chile this rate reaches as much as 100%. While the disease is well-researched from a medical point of view, the two-step mechanism of formation of gallstones is not well studied.

Molecular Dynamic Analysis of Hyaluronic Acid and Phospholipid Interaction in Tribological Surgical Adjuvant Design for Osteoarthritis.

Tribological surgical adjuvants constitute a therapeutic discipline made possible by surgical advances in the treatment of damaged articular cartilage beyond palliative care. The purpose of this study is to analyze interactions between hyaluronic acid and phospholipid molecules, and the formation of geometric forms, that play a role in the facilitated lubrication of synovial joint organ systems. The analysis includes an evaluation of the pathologic state to detail conditions that may be encountered by adjuvants during surgical convalescence.

On morphological selection rule of noisy character applied to model (dis)orderly protein formations.

We propose that the main mechanism controlling the selection rule of model (dis)orderly protein formations, such as non-Kossel crystal growth and aggregation of lysozyme from aqueous solution, is an ion-channeling filter having flicker-noise properties. This filter is originated at the interfaces between growing solidlike object and its external liquid-type phase, and it can be considered as a series of voltage gated ion subchannels. The dynamics of each channel is studied by using both simulation and analytic argumentation lines, and represents a novel thought on how to utilize the presence of constructive-noise sources in protein formation, a field of utmost experimental and technological interest.

Protein crystal's shape and polymorphism prediction within the limits resulting from the exploration of the Miyazawa-Jernigan matrix.

A computer study of the prediction of the protein crystal's shape and polymorphism of crystal's structures within the limits resulting from the exploration of the Miyazawa-Jernigan matrix is presented. In this study, a coarse-graining procedure was applied to prepare a two-dimensional growth unit, where instead of full atom representation of the protein a two-type (hydrophobic-hydrophilic, HP) aminoacidal representation was used. The interaction energies between hydrophobic (E(HH)) aminoacids were chosen from the well-known HP-type models (E(HH)in[-4,-3,-2.

On the protein crystal formation as an interface-controlled process with prototype ion-channeling effect.

A superdiffusive random-walk action in the depletion zone around a growing protein crystal is considered. It stands for a dynamic boundary condition of the growth process and competes steadily with a quasistatic, curvature-involving (thermodynamic) free boundary condition, both of them contributing to interpret the (mainly late-stage) growth process in terms of a prototype ion-channeling effect. An overall diffusion function contains quantitative signatures of both boundary conditions mentioned and indicates whether the new phase grows as an orderly phase or a converse scenario occurs.