Change In Interaction Energy Research Articles

The hierarchical energy landscape of edge dislocation glide in refractory high-entropy alloys

Refractory high-entropy alloys (RHEAs) are considered as potential candidates for high-temperature applications, with the glide resistance of edge dislocations being a crucial factor in determining the high-temperature strength. However, the solid-solution strengthening mechanism of edge dislocations in RHEAs is not fully understood. The existing Labusch-type models mainly focus on the long-range interaction of solute atoms with the dislocation stress field, while there is little attention paid to the short-range interaction in the dislocation core region. Here, we conduct carefully designed atomic simulations to decouple the long-range and short-range interactions in a typical RHEA, NbMoTaW. Furthermore, the total change in solute-dislocation interaction energy is decomposed, and a hierarchical energy landscape is revealed, demonstrating that the short-range interaction at the core region gains more importance in the solid-solution strengthening of edge dislocations in NbMoTaW. Then, we determine the Larkin length, which signifies the transition from size-dependent to size-independent dislocation behavior. The activation barrier extracted from the simulation with the dislocation length above the Larkin length is incorporated into the crystal plasticity model, and the high-temperature yield strength is well predicted by the strengthening from edge dislocations. Our work provides deep insight into the solid-solution strengthening mechanism in random solution solids, elucidating the importance of the local atomic configuration around the dislocation core.

Membrane fouling characteristics and mechanisms in coagulation-ultrafiltration process for treating microplastic-containing water

Microplastics (MPs) are recognized as a significant challenge to water treatment processes due to their ability to adsorb or accumulate alginate foulants, impacting the coagulation-ultrafiltration (CUF) process. In this study, the mechanisms of membrane fouling caused by MPs under varying dosages of polymeric aluminum chloride (PAC) coagulant in the CUF process were investigated. It was revealed that MPs contribute to membrane fouling, which initially intensifies and then alleviates as coagulant concentration increases, with a turning point at 0.05 mM PAC dosage. The most significant alleviation of membrane fouling was observed at 0.2 mM PAC dosage. An in-depth analysis of interfacial interaction energy changes during filtration was conducted using the extended Derjaguin-Landau-Verwey-Overbeek (XDLVO) theory, demonstrating how MPs alter the interaction forces between foulants and the membrane surface, leading to either the exacerbation or mitigation of fouling. Additionally, it was shown that at optimal coagulant concentrations, the presence of MPs promotes the formation of a loose and porous cake layer, disrupting the original structure and creating a more open block structure, thereby alleviating membrane fouling. These findings provide valuable insights for optimizing the CUF process in microplastic-containing water treatment, presenting a novel approach to enhancing efficiency and reducing membrane fouling.

Charge Phenomena in the Elastic Backscattering of Electrons from Insulating Polymers.

Elastic peak electron spectroscopy (EPES) analyzes the line shape of the elastic peak. The reduction in energy of the elastic peak electrons is the result of energy transfer to the target atoms, a phenomenon known as recoil energy. EPES differs from other electron spectroscopies in its unique ability to identify hydrogen in polymers and hydrogenated carbon-based materials. This feature is particularly noteworthy as lighter elements exhibit stronger energy shifts. The energy difference between the positions of the elastic peak of carbon and the elastic peak of hydrogen tends to increase as the kinetic energy of the incident electrons increases. During electron irradiation of an insulating polymer, if the number of secondary electrons emitted from the surface is less than the number of electrons absorbed in the sample, the surface floats energetically until it stabilizes at a potential energy eVs. As a result, the interaction energy changes and modifies the energy difference between the elastic peaks of hydrogen and carbon. In this study, the charge effects are evaluated using the Monte Carlo method to simulate the EPES spectra of electrons interacting with polystyrene and polyethylene.

Pyridyl-Substituted Nitronyl Nitroxides: Comprehensive Magnetochemical and Quantum Chemical Study.

A series of pyridyl-substituted nitronyl nitroxides was synthesized and structurally characterized. A comprehensive magnetochemical and quantum chemical study of extended raw of the nitroxides with different substituents R in the pyridine fragment was performed. It was shown, that temperature-dependent magnetic properties are determined by the short contacts between nitroxide groups of adjacent molecules as well as between nitroxide group and methyl substituents in the pseudo axial positions of imidazoline fragments. Quantum chemistry allows to select the appropriate model of exchange cluster for analysis of experimental magnetic data and evaluation of the exchange interaction parameters. For NN-PyCl the "order-disorder" transition was detected by means of low temperature XRD. The difference in the experimental and calculated exchange interaction energies may serve as an indicator of temperature-induced structural rearrangements. For instance, for methyl substituted nitronyl nitroxide NN-PyMe structural transformations and significant changes in exchange interaction energies were observed.

Controlling the asphaltene precipitation behaviors by changing the position and number of nitrogen in the aromatic heterocyclic pendant of polymers with the assistance of DFT calculations

AbstractAs the largest component in crude oil, asphaltenes are apt to settle out and result in the blockage of pipeline during production and transportation, which largely reduces the safety and economic benefits. In this study, a series of poly(maleic anhydride‐octadecene)s (PMO) amidated by pyrimidine (MD), pyrazine (BQ), pyrazole (BZ), triazole (3DZ), triazine (6J3Q), phenyl triazine (6B3Q) and pyrazolo pyridine (ZBD) were synthesized. The interaction energies between the different polymers and asphaltene were calculated by using density functional theory (DFT). It shows that the greater the number of nitrogen‐containing groups and rings, the higher the interaction energy. Moreover, the position of the nitrogen on the aromatic ring also impacts the interaction energy. The interaction energy between asphaltene and polymer with adjacent N (PMO‐BZ) is larger than that with para‐N (PMO‐BQ) and interstitial N (PMO‐MD). In addition, the performance of polymers on asphaltene precipitation from model oil and crude oil is explored by UV–Vis spectroscopy, turbidity, dynamic light scattering (DLS) and rheological methods. The performance of polymers follows the sequence of PMO‐BZ > PMO‐6J3Q > PMO‐BQ > PMO‐MD > PMO‐6B3Q > PMO‐ZBD, which is not consistent with the change of interaction energy. Apparently, the efficiency of the polymer increases and then declines with the increase of interaction energy. Notably, the polymer (PMO‐BZ) containing monocyclic ring with adjacent N increased the IPP of asphaltenes from 0.363 to 0.800 and reduced the particle size from 1527.2 to 99.7 nm. The interaction energies of PMO‐BZ and PMO‐6J3Q with asphaltene are in the range of 15.87–17.04 KJ/mol, and the polymers with interaction energies in this range are more effective on asphaltene inhibition than the others. Consequently, the interaction energies obtained from DFT calculations can be used to guide the design and synthesis of polymers with nitrogen‐containing heterocyclic pendant for asphaltene inhibition.

Effect analysis of temperature and initial water content on the adsorption and separation of VOCs by ZIF‐8 based on molecular simulation

AbstractVolatile organic compounds (VOCs) have seriously polluted the atmospheric environment and caused harmful effects on human beings, so it is imperative to control oil vapor emissions. Metal organic framework materials, as one of the porous materials, have a good application prospect in the field of gas adsorption separation. In this paper, the effects of temperature and initial water content (IWC) on the adsorption properties of methane (CH4), ethane (C2H6), ethylene (C2H4), propane (C3H8), and propylene (C3H6) by ZIF‐8 were studied by combining the large gauge Monte Carlo (GCMC) and ideal adsorption solution theory. The results show that the higher the temperature is, the lower the adsorption capacity is, the higher the threshold pressure is, and the single molecule interaction energy changes little with temperature. But pore volume is still the main influencing factor. The IWC also reduces the saturated adsorption capacity. Preloaded water molecules can enhance the electrostatic interaction at low pressure, thus affecting the adsorption heat and interaction energy of single molecules. Overall, these findings provide valuable mechanistic insights into the effects of temperature and IWC on the adsorption properties of ZIF‐8 for VOCs.

Effects of Water Content on the Transport and Thermodynamic Properties of Phosphonium Ionic Liquids.

We present a numerical investigation of the influence of water content on the dynamic properties of a family of phosphonium-based room-temperature ionic liquids. The study presents a compelling correlation between structural changes in water-ionic liquid solutions and thermodynamic and transport properties across diverse systems. The results for phosphonium ionic liquids are compared with 1-butyl-3-methylimidazolium hexaphosphate ([bmim]PF6) as a reference. Through this approach, phosphonium cation structure-related characteristics can be identified and placed within the broader context of ionic liquids. These insights are underpinned by observed changes in interaction energy, boiling point, diffusion rate, and viscosity, highlighting the crucial role of water molecules in weakening the strength of interactions between ions within the ionic liquid. The investigation also explains temperature-dependent trends in phosphonium cations, showing that alkyl group length and molecular symmetry are important tuning parameters for the strength of Coulomb interactions. These results contribute to a refined understanding of phosphonium ionic liquid behavior in the presence of water, offering valuable insights for optimizing their use in diverse fields.

An efficient solution based on the synergistic effects of nickel foam in NiFe-LDH nanosheets for oil/water separation

Efficient oil-water separation has always been a research hotspot in the field of environmental studies. Employing a one-step hydrothermal approach, NiFe-layered double hydroxides (LDH) nanosheets were synthesized on nickel foam substrates. The resulting NiFe-LDH/NF membrane exhibited rejection rates exceeding 99% across six diverse oil-water mixtures, concurrently demonstrating a remarkable ultra-high flux of 1.4 × 106 L·m−2·h−1. This flux value significantly surpasses those documented in existing literature, maintaining stable performance over 1000 manual filtration cycles. These breakthroughs stem from the synergistic interplay among the three-dimensional channels of the nickel foam, the nanosheets, and the hydration layer. By leveraging the pore size of the foam to enhance the functionality of the hydration layer, the conventional trade-off between permeability and selectivity was transformed into a balanced force relationship between the hydration layer and the oil phase. The operational and failure mechanisms of the hydration layer were examined using the prepared NiFe-LDH/NF membrane, validating the correlation between oil phase viscosity and density with hydration layer rupture. Additionally, an extended Derjaguin-Landau-Verwey-Overbeek (XDLVO) theory was employed to investigate changes in interaction energy, further reinforcing the study's findings. This research contributes novel insights and assistance to the comprehension and application of hydration layers in other membrane studies dedicated to oil-water separation.

Study on the Effect of Cations on the Surface Energy of Nano-SiO2 Particles for Oil/Gas Exploration and Development Based on the Density Functional Theory.

Although nano SiO2 exhibits excellent application potential in the field of oil and gas exploration and development, such as drilling fluid, enhanced oil/gas recovery, etc., it is prone to agglomeration and loses its effectiveness due to the action of cations in saline environments of oil and gas reservoirs. Therefore, it is crucial to study the mechanism of the change in energy between nano SiO2 and cations for its industrial application. In this paper, the effect of cations (Na+, K+, Ca2+, and Mg2+) on the surface energy of nano SiO2 particles is investigated from the perspective of molecular motion and electronic change by density functional theory. The results are as follows: Due to the electrostatic interactions, cations can migrate towards the surface of nano SiO2 particles. During the migration process, monovalent cations are almost unaffected by water molecules, and they can be directly adsorbed on the surface by nano SiO2 particles. However, when divalent cations migrate from a distance to the surface of nano SiO2 particles, they can combine with water molecules to create an energy barrier, which can prevent them from moving forward. When divalent cations break through the energy barrier, the electronic kinetic energy between them and nano SiO2 particles changes more strongly, and the electrons carried by them are more likely to break through the edge of the atomic nucleus and undergo charge exchange with nano SiO2 particles. The change in interaction energy is more intense, which can further disrupt the configuration stability of nano SiO2. The interaction energy between cations and nano SiO2 particles mainly comes from electrostatic energy, followed by Van der Waals energy. From the degree of influence of four cations on nano SiO2 particles, the order from small to large is as follows: K+ < Na+ < Mg2+ < Ca2+. The research results can provide a theoretical understanding of the interaction between nano SiO2 particles and cations during the application of nano SiO2 in the field of oil and gas exploration and development.

On the origin of Sanchez-Lacombe equation of state theory in hydrostatic strain energy model for rubber-like materials

To capture the volume deformation of rubber-like materials, the strain energy density (SED) function of a compressible hyperelastic model is formulated as the hydrostatic/liquid-like term from interchain interaction changes plus the compressible elastic term owing to elastic deformation of crosslinking network. Notably, the former term dominates volume responses. Although the physics of the hydrostatic term is relatively clear, to our knowledge, few physically-based models are available. However, in our previous work (Liu and Lu, 2023), we constructed a physically-based hydrostatic SED function inspired by the Flory-Orwoll-Vrij equation of state (EOS) theory for pure polymer fluids, and proposed the general strategy for developing hydrostatic functions according to the EOS theories. Sanchez-Lacombe EOS theory (note: a type of lattice-fluid EOS theory) inspired this work. We assume: (i) a rubber-like material consists of polymer segments occupying lattice sites and unoccupied/vacant lattice sites, and the compressibility of the material corresponds to changes in vacant sites fraction; (ii) the hydrostatic strain energy is associated with the interchain interaction energy change and the mixing entropy change between network and vacant sites. According to the Helmholtz free energy in Sanchez-Lacombe EOS theory and limiting our attention to the isothermal condition, another physically-based hydrostatic SED function is constructed; a specific compressible hyperelastic model is provided by further combining compressible 8-chain elastic SED function. The basic framework of this compressible model is inherently consistent with the Flory-Rehner framework for swollen elastomers. Our model provides good predictions for volume deformation data of ten different rubber-like materials in hydrostatic compression (HC), uniaxial tension (UT), and constrained uniaxial compression (CUC). The proposed model reveals that HC, CUC, or uniaxial compression correspond to the entropy-decreasing process and they all are controlled by entropy changes; while for UT, equibiaxial tension, or pure shear, the entropy first increases and then decreases, and the interchain interaction energy and entropy changes control the responses for initial small stretches and remaining large stretches, respectively. This study aims to provide a new physical insight and a valid physically-based hydrostatic SED function for the compressibility of rubber-like materials.

Multiple hydrogen-bonded dimers: are only the frontier atoms relevant?

Non-frontier atom exchanges in hydrogen-bonded aromatic dimers can induce significant interaction energy changes (up to 6.5 kcal mol-1). Our quantum-chemical analyses reveal that the relative hydrogen-bond strengths of N-edited guanine-cytosine base pair isosteres, which cannot be explained from the frontier atoms, follow from the charge accumulation in the monomers.

Engineering the Relatively Conserved Residues in Active Site Architecture of Thermophilic Chitinase SsChi18A Enhanced Catalytic Activity.

Chitinase plays a vital role in the efficient biotransformation of the chitin substrate. This study aimed to modify and elucidate the contribution of the relatively conserved residues in the active site architecture of a thermophilic chitinase SsChi18A from Streptomyces sp. F-3 in processive catalysis. The enzymatic activity on colloidal chitin increased to 151%, 135%, and 129% in variants Y286W, E287A, and K186A compared with the wild type (WT). Also, the apparent processive parameter G2/G1 was lower in the variants compared to the WT, indicating the essential role of Tyr-286, Glu-287, and Lys-186 in processive catalysis. Additionally, the enzymatic activity on the crystalline chitin of F48W and double mutants F48W/Y209F and F48W/Y286W increased by 35%, 16%, and 36% compared with that for WT. Molecular dynamics simulations revealed that the driving force of processive catalysis might be related to the changes in interaction energy. This study provided a rational design strategy targeting relatively conserved residues to enhance the catalytic activity of GH18 processive chitinases.

Developing similarity matrices for antibody-protein binding interactions.

The inventions of AlphaFold and RoseTTAFold are revolutionizing computational protein science due to their abilities to reliably predict protein structures. Their unprecedented successes are due to the parallel consideration of several types of information, one of which is protein sequence similarity information. Sequence homology has been studied for many decades and depends on similarity matrices to define how similar or different protein sequences are to one another. A natural extension of predicting protein structures is predicting the interactions between proteins, but similarity matrices for protein-protein interactions do not exist. This study conducted a mutational analysis of 384 non-redundant antibody-protein antigen complexes to calculate antibody-protein interaction similarity matrices. Every important residue in each antibody and each antigen was mutated to each of the other 19 commonly occurring amino acids and the percentage changes in interaction energies were calculated using three force fields: CHARMM, Amber, and Rosetta. The data were used to construct six interaction similarity matrices, one for antibodies and another for antigens using each force field. The matrices exhibited both commonalities, such as mutations of aromatic and charged residues being the most detrimental, and differences, such as Rosetta predicting mutations of serines to be better tolerated than either Amber or CHARMM. A comparison to nine previously published similarity matrices for protein sequences revealed that the new interaction matrices are more similar to one another than they are to any of the previous matrices. The created similarity matrices can be used in force field specific applications to help guide decisions regarding mutations in protein-protein binding interfaces.

Molecular study on diffusion behavior and performance recovery of aged asphalt binder containing functional rejuvenators

In hot in-place recycling (HIR) technology, there are many shortcomings and challenges such as low mixing temperature, short mixing time and less virgin asphalt binder, demanding multifunctional rejuvenators with higher diffusion rates. Therefore, there is an urgent need to develop a rejuvenator that balances diffusion rate and performance recovery. In this study, molecular dynamics (MD) simulation was employed to establish the basic structure of oil fractions, including chain alkanes, cycloalkanes and aromatic hydrocarbons. To improve the diffusion rate of rejuvenators, functional groups in penetrants and surfactants, such as hydroxyl, carboxyl, amide, ether, and ester groups, were incorporated into the basic structure for artificial design and enhancement. The diffusion rates of the primary and enhanced structures were investigated, and the internal factors for diffusion were analyzed. Furthermore, two rejuvenation methods for rejuvenators were proposed based on the changes in non-bond interaction energy in different asphalt binder systems. Moreover, the performance recovery of different rejuvenators were investigated. The results show that the diffusion rate of chain alkanes in the basic structure is the fastest, while that of aromatic hydrocarbons is the slowest. When ether and ester groups are used as enhanced structures, the diffusion rates of chain alkanes increase by 34.7% and 61.1%, respectively. Regarding performance recovery, chain alkanes exhibit the best performance recovery effect, which is further enhanced when ether and ester groups are employed as enhanced structures.

A physically-based hydrostatic strain energy model for rubber-like materials inspired by Flory-Orwoll-Vrij equation of state theory

In a compressible hyperelastic model for rubber-like materials, the strain energy function is generally composed of the hydrostatic part corresponding to changes in interchain interactions and the compressible elastic part attributable to the network structure. It is well known that the hydrostatic part dominates the compressibility of the material. In this study, inspired by the Flory-Orwoll-Vrij (FOV) equation of state (EOS) theory for pure polymer liquids (note: a cell-like EOS theory), we assume that (i) the compressibility of rubber-like materials corresponds to changes in free volume of polymer chain segments; (ii) the hydrostatic strain energy of a rubber-like solid is attributable to changes in interchain interaction energy and chain segments’ external motion degrees of freedom (the latter solely depends on interchain forces). With a focus on the reversible isothermal deformation process, we construct a physically-based hydrostatic strain energy function based on the Helmholtz free energy formulation in FOV EOS theory. With a view towards applications, we provide a specific compressible hyperelastic model by incorporating the new hydrostatic strain energy function and compressible eight-chain model, where the latter is utilized as the elastic part of the strain energy function. Our model is capable of predicting various volume data of rubber-like materials from the literature, such as the nonlinear pressure-volume response at finite volume changes in hydrostatic compression (HC), the volume change-stretch and stress-stretch data in uniaxial tension (UT), and the stress-volume data in constrained uniaxial compression (CUC). Given the severely limited volume change data for finite stretches in UT and other modes of deformation, we simulate the volume change-volume modulus-stretch responses in UT, equibiaxial tension (ET), pure shear (PS), and uniaxial compression (UC) over their respective theoretical range of stretch and successfully predict some available (qualitative) experimental observations. Together with the simulations of the volume change-stretch responses in UT, ET, PS, and UC based on the Ogden’s and Bischoff et al.’s compressible models, we summarize the characteristics of these responses and analyze the possible deformation mechanisms. These simulations can provide some guidance for future corresponding experiments. Finally, we analyze the deformation mechanisms of HC, CUC, UT, ET, PS, and UC by simulating the responses for total strain energy and its components. This study provides a new physical picture and corresponding theoretical model for the hydrostatic strain energy function of rubber-like materials and finally proposes the general research strategy for constructing new hydrostatic strain energy functions based on the EOS theories for pure polymer liquids.

Molecular Crowders Can Induce Collapse in Hydrophilic Polymers via Soft Attractive Interactions.

A comprehensive understanding of protein folding and biomolecular self-assembly in the intracellular environment requires obtaining a microscopic view of the crowding effects. The classical view of crowding explains biomolecular collapse in such an environment in terms of the entropic solvent excluded volume effects subjected to hard-core repulsions exerted by the inert crowders, neglecting their soft chemical interactions. In this study, the effects of nonspecific, soft interactions of molecular crowders in regulating the conformational equilibrium of hydrophilic (charged) polymers are examined. Using advanced molecular dynamics simulations, collapse free energies of an uncharged, a negatively charged, and a charge-neutral 32-mer generic polymer are computed. The strength of the polymer-crowder dispersion energy is modulated to examine its effect on polymer collapse. The results show that the crowders preferentially adsorb and drive the collapse of all three polymers. The uncharged polymer collapse is opposed by the change in solute-solvent interaction energy but is overcompensated by the favorable change in the solute-solvent entropy as observed in hydrophobic collapse. However, the negatively charged polymer collapses with a favorable change in solute-solvent interaction energy due to reduction in the dehydration energy penalty as the crowders partition to the polymer interface and shield the charged beads. The collapse of a charge-neutral polymer is opposed by the solute-solvent interaction energy but is overcompensated by the solute-solvent entropy change. However, for the strongly interacting crowders, the overall energetic penalty decreases since the crowders interact with polymer beads via cohesive bridging attractions to induce polymer collapse. These bridging attractions are found to be sensitive to the binding sites of the polymer, since they are absent in the negatively charged or uncharged polymers. These interesting differences in thermodynamic driving forces highlight the crucial role of the chemical nature of the macromolecule as well as of the crowder in determining the conformational equilibria in a crowded milieu. The results emphasize that the chemical interactions of the crowders should be explicitly considered to account for the crowding effects. The findings have implications in understanding the crowding effects on the protein free energy landscapes.

Experimental and Computational Investigation of Benperidol and Droperidol Solid Solutions in Different Crystal Structures

We present an experimental and computational study of solid solution formation between structurally highly similar active pharmaceutical ingredients droperidol and benperidol in nonsolvates, dihydrates, and several solvates formed by these compounds. We demonstrate that the formation of solid solutions strongly depends on the crystal structure of the phase. In some of the structures, almost complete replacement of benperidol with droperidol can be achieved, whereas in other structures, the replacement is possible only up to a limited molar ratio. However, only limited replacement of droperidol with benperidol can be achieved and only in some of the structures. The solid solution formation is primarily determined by the change in intermolecular interaction energy resulting from the molecule replacement. Only structures where molecule replacement allows the formation of efficient intermolecular interactions can be obtained experimentally. The results indicate that the energy requirements of intermolecular interaction changes to obtain solid solutions in the nonsolvated phase are less strict than those for solvates.

The role of limonene in the branching of straight chains in low-octane hydrocarbons

Limonene has great potential as a bio-additive. It has physical characteristics resembling those of fuel oil and has a molecular structure that could potentially allow limonene to be used as an octane booster. With an octane number of only 88, limonene is able to increase RON. The increase was caused by limonene stimulation, which improved the molecular structure, resulting in straight-chain branching. To investigate the molecular interactions between limonene and blended fuel, n-heptane was chosen as a fuel to represent low-RON fuel. Limonene and n-heptane were blended, so the effect of limonene on n-heptane could be observed. Analysis was conducted by using HyperChem, which was validated by the experiment to calculate the important molecular properties of each fuel blend. Spaya.ai artificial software was used to track the straight-chain branching schematic routes and then the mechanisms were detected. The results showed that there was a significant increase in RON in the blending of n-heptane and limonene. Limonene at a concentration of only 1% was able to increase the RON of n-heptane from 0 to 91.15, which exceeds RON of limonene. This increase was due to the change in molecular interaction energy causing a change in the shape of the molecular structures.

Ethylene glycol energetically disfavours oligomerization of pseudoisocyanine dyestuffs at crowded concentrations.

The intriguing role of the intracellular crowded environment in regulating protein aggregation remains elusive. The convolution of several factors such as the protein sequence-dependence, crowder's shape and size and diverse intermolecular interactions makes it complex to identify systematic trends. One of the ways to simplify the problem is to study a synthetic model for self-assembling proteins. In this study, we examine the aggregation behaviour of the cationic pseudoisocyanine chloride (PIC) dyestuff which is known to self-assemble and form fibril-like J-aggregates in aqueous solutions, similar to those formed by amyloid-forming proteins. Prior experimental studies have shown that polyethylene glycol impedes and Ficoll-400 promotes the self-assembly of PIC dyes. To achieve molecular insights, we examine the effect of crowding by ethylene glycol on the solvation thermodynamics of oligomerization of dyes into H-type and J-type oligomers using extensive molecular dynamics simulations. The binding free energy calculations show that the formation of J-oligomers is more favourable than that of H-oligomers in water. The stability of H- and J- tetramers and pentamers decreases in crowded solutions. The formation of oligomers is supported by the favourable change in dye-solvent interaction energy in both pure water and aqueous ethylene glycol solution although it is opposed by the reduced dye-solvent entropy. Ethylene glycol, as a molecular crowder, disfavours the H- as well as J-oligomerization via preferential binding to the dye oligomers. An unfavourable change in dye-crowder and dye-dye interaction energy on dye association makes the H-oligomer formation less favourable in crowded solution than in pure water solution. In the case of J-oligomers, however, the unfavourable change in dye-crowder interaction energy primarily contributes to making total dye-solvent energy unfavourable. The results are supported by isothermal titration calorimetry measurements where the binding of ethylene glycol to PIC molecules is found to be endothermic. The results provide an emerging view that a crowded environment can disfavour self-assembly of PIC dyes by interactions with the oligomeric states. The findings have implications in understanding the role of a crowded environment in shaping the free energy landscapes of proteins.

Energetic and atomic structural analyses of the screw dislocation absorption at tilt grain boundaries in BCC-Fe.

The dislocation-grain boundary (GB) interaction plays an important role in GB-related plasticity. Therefore, an atomistic investigation of the interaction provides a deeper understanding of the strength and fracture of polycrystalline metals. In this study, we investigated the absorption of a screw dislocation with a Burgers vector perpendicular to the GB normal and the corresponding symmetric tilt grain boundaries (STGBs) in BCC-Fe based on molecular static simulations focusing on the STGB-dislocation interaction energy and atomistic structural changes at GB. The STGB-screw dislocation interaction depends on the energetical stability of the STGB against the GB shift along the Burgers vector direction. When the interaction exhibited a large attractive interaction energy, the dislocation dissociation and the GB shift along the Burgers vector direction occurred simultaneously. The interaction energy reveals that the interaction depends on the energetical stability of the STGB in terms of the GB shift in addition to the geometrical descriptor of the GB type, such as the Σ value. The same behavior was also obtained in the reaction when the second dislocation was introduced. We also discuss the screw dislocation absorption and rearrangement of the GB atomistic structure in STGB from an energetic viewpoint.