Optimizing biodegradable plastics: Molecular dynamics insights into starch plasticization with glycerol and oleic acid.

Petroleum-based plastics dominate everyday life, necessitating the exploration of natural polymers as alternatives. Starch, abundant and biodegradable, is a promising raw material. However, understanding the molecular mechanisms underlying starch plasticization has proven challenging. To address this, we employ molecular dynamics simulations, focusing on amylose as a model. Our comprehensive evaluation revealed that chain size affects solubility, temperature influenced diffusivity and elastic properties, and oleic acid expressed potential as an alternative plasticizer. Furthermore, blending glycerol or oleic acid with water suggested the enhancement amylose's elasticity. These findings contribute to the design of sustainable and improved biodegradable plastics.

Assessment of the Wolf method using the Stillinger-Lovett sum rules: From strong electrolytes to weakly charged colloidal dispersions.

The Ewald method has been the cornerstone in molecular simulations for modeling electrostatic interactions of charge-stabilized many-body systems. In the late 1990s, Wolf and collaborators developed an alternative route to describe the long-range nature of electrostatic interactions; from a computational perspective, this method provides a more efficient and straightforward way to implement long-range electrostatic interactions than the Ewald method. Despite these advantages, the validity of the Wolf potential to account for the electrostatic contribution in charged fluids remains controversial. To alleviate this situation, in this contribution, we implement the Wolf summation method to both electrolyte solutions and charged colloids with moderate size and charge asymmetries in order to assess the accuracy and validity of the method. To this end, we verify that the proper selection of parameters within the Wolf method leads to results that are in good agreement with those obtained through the standard Ewald method and the theory of integral equations of simple liquids within the so-called hypernetted chain approximation. Furthermore, we show that the results obtained with the original Wolf method do satisfy the moment conditions described by the Stillinger-Lovett sum rules, which are directly related to the local electroneutrality condition and the electrostatic screening in the Debye-Hückel regime. Hence, the fact that the solution provided by the Wolf method satisfies the first and second moments of Stillinger-Lovett proves, for the first time, the reliability of the method to correctly incorporate the electrostatic contribution in charge-stabilized fluids. This makes the Wolf method a powerful alternative compared to more demanding computational approaches.

Hot Spots and Their Contribution to the Self-Assembly of the Viral Capsid: In Silico Prediction and Analysis.

The viral capsid is a macromolecular complex formed by a defined number of self-assembled proteins, which, in many cases, are biopolymers with an identical amino acid sequence. Specific protein-protein interactions (PPI) drive the capsid self-assembly process, leading to several distinct protein interfaces. Following the PPI hot spot hypothesis, we present a conservation-based methodology to identify those interface residues hypothesized to be crucial elements on the self-assembly and thermodynamic stability of the capsid. We validate the predictions through a rigorous physical framework which integrates molecular dynamics simulations and free energy calculations by Umbrella sampling and the potential of mean force using an all-atom molecular representation of the capsid proteins of an icosahedral virus in an explicit solvent. Our results show that a single mutation in any of the structure-conserved hot spots significantly perturbs the quaternary protein-protein interaction, decreasing the absolute value of the binding free energy, without altering the protein's secondary nor tertiary structure. Our conservation-based hot spot prediction methodology can lead to strategies to rationally modulate the capsid's thermodynamic properties.

An Amphotericin B Derivative Equally Potent to Amphotericin B and with Increased Safety.

Amphotericin B is the most potent antimycotic known to date. However due to its large collateral toxicity, its use, although long standing, had been limited. Many attempts have been made to produce derivatives with reduced collateral damage. The molecular mechanism of polyene has also been closely studied for this purpose and understanding it would contribute to the development of safe derivatives. Our study examined polyene action, including chemical synthesis, electrophysiology, pharmacology, toxicology and molecular dynamics. The results were used to support a novel Amphotericin B derivative with increased selectivity: L-histidine methyl ester of Amphotericin B. We found that this derivative has the same form of action as Amphotericin B, i.e. pore formation in the cell membrane. Its reduced dimerization in solution, when compared to Amphotericin B, is at least partially responsible for its increased selectivity. Here we also present the results of preclinical tests, which show that the derivative is just as potent as Amphotericin B and has increased safety.

Renormalized jellium mean-field approximation for binary mixtures of charged colloids.

In this work the renormalized jellium model of colloidal suspensions, originally proposed by Trizac and Levin [Phys. Rev. E 69, 031403 (2004)], is extended to study mechanisms of charge renormalization in binary mixtures of charged colloids. We here apply our recent reformulation that introduces the requirement of self-consistency directly into the Poisson-Boltzmann equation, i.e., the background charge is explicitly replaced by the effective one, thus facilitating the whole charge renormalization scheme. We briefly discuss the reformulated model for monodisperse charged suspensions composed of either spheres or rods. In particular, we put emphasis on the effects of the surface charge variation, mixture composition, and particle size on the charge regulation of charge-stabilized colloidal suspensions.