Ion-Specific Effects on Ion and Polyelectrolyte Solvation.

Ion-specific effects on aqueous solvation of monovalent counter ions, Na , K , Cl , and Br , and two model polyelectrolytes (PEs), poly(styrene sulfonate) (PSS) and poly(diallyldimethylammonium) (PDADMA) were here studied with ab initio molecular dynamics (AIMD) and classical molecular dynamics (MD) simulations based on the OPLS-aa force-field which is an empirical fixed point-charge force-field. Ion-specific binding to the PE charge groups was also characterized. Both computational methods predict similar response for the solvation of the PEs but differ notably in description of ion solvation.

Positive Trions in InP/ZnSe/ZnS Colloidal Nanocrystals.

InP-based colloidal nanocrystals are being developed as an alternative to cadmium-based materials. However, their optical properties have not been widely studied. In this paper, the fundamental magneto-optical properties of InP/ZnSe/ZnS nanocrystals are investigated at cryogenic temperatures.

Spidroins under the Influence of Alcohol: Effect of Ethanol on Secondary Structure and Molecular Level Solvation of Silk-Like Proteins.

Future sustainable materials based on designer biomolecules require control of the solution assembly, but also interfacial interactions. Alcohol treatments of protein materials are an accessible means to this, making understanding of the process at the molecular level of seminal importance. We focus here on the influence of ethanol on spidroins, the main proteins of silk.

Triblock Proteins with Weakly Dimerizing Terminal Blocks and an Intrinsically Disordered Region for Rational Design of Condensate Properties.

Condensates are molecular assemblies that are formed through liquid-liquid phase separation and play important roles in many biological processes. The rational design of condensate formation and their properties is central to applications, such as biosynthetic materials, synthetic biology, and for understanding cell biology. Protein engineering is used to make a triblock structure with varying terminal blocks of folded proteins on both sides of an intrinsically disordered mid-region.

Computer Simulations of Deep Eutectic Solvents: Challenges, Solutions, and Perspectives.

Deep eutectic solvents (DESs) are one of the most rapidly evolving types of solvents, appearing in a broad range of applications, such as nanotechnology, electrochemistry, biomass transformation, pharmaceuticals, membrane technology, biocomposite development, modern 3D-printing, and many others. The range of their applicability continues to expand, which demands the development of new DESs with improved properties. To do so requires an understanding of the fundamental relationship between the structure and properties of DESs.

Changes in the Local Conformational States Caused by Simple Na and K Ions in Polyelectrolyte Simulations: Comparison of Seven Force Fields with and without NBFIX and ECC Corrections.

Electrostatic interactions have a determining role in the conformational and dynamic behavior of polyelectrolyte molecules. In this study, anionic polyelectrolyte molecules, poly(glutamic acid) (PGA) and poly(aspartic acid) (PASA), in a water solution with the most commonly used K or Na counterions, were investigated using atomistic molecular dynamics (MD) simulations. We performed a comparison of seven popular force fields, namely AMBER99SB-ILDN, AMBER14SB, AMBER-FB15, CHARMM22*, CHARMM27, CHARMM36m and OPLS-AA/L, both with their native parameters and using two common corrections for overbinding of ions, the non-bonded fix (NBFIX), and electronic continuum corrections (ECC).

Effects of Amino Acid Side-Chain Length and Chemical Structure on Anionic Polyglutamic and Polyaspartic Acid Cellulose-Based Polyelectrolyte Brushes.

We used atomistic molecular dynamics (MD) simulations to study polyelectrolyte brushes based on anionic α,L-glutamic acid and α,L-aspartic acid grafted on cellulose in the presence of divalent CaCl salt at different concentrations. The motivation is to search for ways to control properties such as sorption capacity and the structural response of the brush to multivalent salts. For this detailed understanding of the role of side-chain length, the chemical structure and their interplay are required.

Optically detected magnetic resonance in CdSe/CdMnS nanoplatelets.

Core/shell CdSe/(Cd,Mn)S colloidal nanoplatelets containing magnetic Mn2+ ions are investigated by the optically detected magnetic resonance technique, combining 60 GHz microwave excitation and photoluminescence detection. Resonant heating of the Mn spin system is observed. We identify two mechanisms of optical detection, via variation of either the photoluminescence polarization or its intensity in an external magnetic field.

Magneto-Optics of Excitons Interacting with Magnetic Ions in CdSe/CdMnS Colloidal Nanoplatelets.

Excitons in diluted magnetic semiconductors represent excellent probes for studying the magnetic properties of these materials. Various magneto-optical effects, which depend sensitively on the exchange interaction of the excitons with the localized spins of the magnetic ions can be used for probing. Here, we study core/shell CdSe/(Cd,Mn)S colloidal nanoplatelets hosting diluted magnetic semiconductor layers.

Influence of Calcium Binding on Conformations and Motions of Anionic Polyamino Acids. Effect of Side Chain Length.

Investigation of the effect of CaCl salt on conformations of two anionic poly(amino acids) with different side chain lengths, poly-(α-l glutamic acid) (PGA) and poly-(α-l aspartic acid) (PASA), was performed by atomistic molecular dynamics (MD) simulations. The simulations were performed using both unbiased MD and the Hamiltonian replica exchange (HRE) method. The results show that at low CaCl concentration adsorption of Ca ions lead to a significant chain size reduction for both PGA and PASA.

Overbinding and Qualitative and Quantitative Changes Caused by Simple Na and K Ions in Polyelectrolyte Simulations: Comparison of Force Fields with and without NBFIX and ECC Corrections.

Overbinding of ions is a common and well-known problem in classical molecular dynamics simulations. One of its main causes is the absence of electronic polarizability in the force fields. The current approaches for minimizing overbinding typically either retain the original charges and use an ad hoc readjustment of the Lennard-Jones parameters as done in the nonbonded fix (NBFIX) approach or rescale the charges using a theoretical framework.

Mineralization of phosphorylated cellulose: crucial role of surface structure and monovalent ions for optimizing calcium content.

Cellulose can be phosphorylated to produce organic matrices with highly adsorptive properties for, e.g., biocompatible materials for biomedical applications.

Molecular-Level Insight into the Interaction of Phospholipid Bilayers with Cellulose.

Molecular-level insight into the interactions of phospholipid molecules with cellulose is crucial for the development of novel cellulose-based materials for wound dressing. Here we employ the state-of-the-art computer simulations to unlock for the first time the molecular mechanisms behind such interactions. To this end, we performed a series of atomic-scale molecular dynamics simulations of phospholipid bilayers on a crystalline cellulose support at various hydration levels of the bilayer leaflets next to the cellulose surface.

Molecular dynamics simulations of oligoester brushes: the origin of unusual conformations.

We present results from all-atom molecular dynamics simulations for the structural properties of oligomeric lactic acid chains (OLA) grafted to the surface of cellulose nanocrystals (CNCs) and immersed in the melt of polylactic acid (PLA). Earlier, we have found that the distribution of free ends of OLA molecules is bimodal [Glova et al., Polym.

Influence of specific intermolecular interactions on the thermal and dielectric properties of bulk polymers: atomistic molecular dynamics simulations of Nylon 6.

Specific intermolecular interactions, in particular H-bonding, have a strong influence on the structural, thermal and relaxation characteristics of polymers. We report here the results of molecular dynamics simulations of Nylon 6 which provides an excellent example for the investigation of such an influence. To demonstrate the effect of proper accounting for H-bonding on bulk polymer properties, the AMBER99sb force field is used with two different parametrization approaches leading to two different sets of partial atomic charges.

Optically Addressable Silicon Vacancy-Related Spin Centers in Rhombic Silicon Carbide with High Breakdown Characteristics and ENDOR Evidence of Their Structure.

We discovered a family of uniaxially oriented silicon vacancy-related centers with S=3/2 in a rhombic 15R-SiC crystalline matrix. We demonstrate that these centers exhibit unique characteristics such as optical spin alignment up to the temperatures of 250°C. Thus, the range of robust optically addressable vacancy-related spin centers is extended to the wide class of rhombic SiC polytypes.

Cellulose Nanofibrils and Mechanism of their Mineralization in Biomimetic Synthesis of Hydroxyapatite/Native Bacterial Cellulose Nanocomposites: Molecular Dynamics Simulations.

Molecular dynamics (MD) simulation of a nanofibril of native bacterial cellulose (BC) in solutions of mineral ions is presented. The supersaturated calcium-phosphate (CP) solution with the ionic composition of hydroxyapatite and CaCl2 solutions with the concentrations below, equal to, and above the solubility limits are simulated. The influence of solvation models (TIP3P and TIP4P-ew water models) on structural characteristics of the simulated nanofibril and on the crystal nucleation process is assessed.

Interactions binding mineral and organic phases in nanocomposites based on bacterial cellulose and calcium phosphates.

The interactions responsible for the adhesion of calcium phosphate (CP) nanocrystals and bacterial cellulose (BC) nanofibrils in the composite material obtained by mixing aqueous suspensions of presynthesized CP and BC and the dependence of these interactions on the CP morphology and chemical structure have been elucidated by molecular mechanics calculations of the CP-BC interfacial structures. The interactions between the superficial CP and BC crystal layers have been simulated. Two crystalline CP structures (i.

Recombination processes in systems based on doped ionic crystals with impurity-related nanostructures.

Recombination processes leading to the tunnelling afterglow and photostimulated luminescence in systems based on host ionic crystals with impurity-related nanostructures-promising phosphors for x-ray storage-were studied by means of luminescence, EPR and optically detected magnetic resonance. It was found that in the x-ray irradiated CsBr:Eu and CsBr:Pb crystals the energy released in the spin-dependent tunnelling recombination of electron-hole pairs and self-trapped excitons in the host crystal is directionally transferred to the impurity-related low-dimensional structures. To identify the origin of recombining electron and hole centres, their EPR spectra were detected by monitoring the tunnelling afterglow and the photostimulated luminescence including the emission bands of the low-dimensional structures.

Use of models of biomacromolecule separation in AMT database generation for shotgun proteomics.

Generation of a complex proteome database requires use of powerful analytical methods capable of following rapid changes in the proteome due to changing physiological and pathological states of the organism under study. One of the promising technologies with this regard is the use of so-called Accurate Mass and Time (AMT) tag peptide databases. Generation of an AMT database for a complex proteome requires combined efforts by many research groups and laboratories, but the chromatography data resulting from these efforts are tied to the particular experimental conditions and, in general, are not transferable from one platform to another.

[Postpericardiotomy syndrome: risk factors and methods of diagnosis].

This study was designed to identify major risk factors of PCTS and elucidate the possibility of early laboratory diagnosis of this syndrome for the choice of optimal therapeutic strategy. Retrospective analysis covered medical records of 500 patients who had experienced open heart surgery. Prospective studies included 60 patients of whom 50 had clinical manifestations of PCTS.

[Combined effects of psychoemotional stress and carbon monoxide in experiments].

Psychoemotional stress and exposure to various concentrations of carbon monoxide are antagonists or act independently. The results necessitate changes in MAC for carbon monoxide in air of workplace.

[Use of dispersion analysis in the assessment of combined effect of low levels of carbon monoxide and psychoemotional stress in chronic experiment].

The article deals with evaluation of joint effects by means of dispersion analysis. The experimental study covered joint effects caused by low levels of carbon oxide (MAC and those 3 times lower) and specific psychoemotional stress in white rats. The studied parameters described activities of the central nervous, cardiovascular and immune systems.