Behavior Of Solutions Research Articles

Insights into mechanisms of MALT1 allostery from NMR and AlphaFold dynamic analyses

Mucosa-associated lymphoid tissue lymphoma-translocation protein 1 (MALT1) is an attractive target for the development of modulatory compounds in the treatment of lymphoma and other cancers. While the three-dimensional structure of MALT1 has been previously determined through X-ray analysis, its dynamic behaviour in solution has remained unexplored. We present here dynamic analyses of the apo MALT1 form along with the E549A mutation. This investigation used NMR 15N relaxation and NOE measurements between side-chain methyl groups. Our findings confirm that MALT1 exists as a monomer in solution, and demonstrate that the domains display semi-independent movements in relation to each other. Our dynamic study, covering multiple time scales, along with the assessment of conformational populations by Molecular Dynamic simulations, Alpha Fold modelling and PCA analysis, put the side chain of residue W580 in an inward position, shedding light at potential mechanisms underlying the allosteric regulation of this enzyme.

GCMe: Efficient Implementation of the Gaussian Core Model with Smeared Electrostatic Interactions for Molecular Dynamics Simulations of Soft Matter Systems.

In recent years, molecular dynamics (MD) simulations have emerged as an essential tool for understanding the structure, dynamics, and phase behavior of charged soft matter systems. To explore phenomena across greater length and time scales in MD simulations, molecules are often coarse-grained for better computational performance. However, commonly used force fields represent particles as hard-core interaction centers with point charges, which often overemphasizes the packing effect and short-range electrostatics, especially in systems with bulky deformable organic molecules and systems with strong coarse-graining. This underscores the need for an efficient soft-core model to physically capture the effective interactions between coarse-grained particles. To this end, we implement a soft-core model uniting the Gaussian core model with smeared electrostatic interactions that is phenomenologically equivalent to recent theoretical models. We first parametrize it generically using water as the model solvent. Then, we benchmark its performance in the OpenMM toolkit for different boundary conditions to highlight a computational speedup of up to 34 × compared to commonly used force fields and existing implementations. Finally, we demonstrate its utility by investigating how boundary polarizability affects the adsorption behavior of a polyelectrolyte solution on perfectly conducting and nonmetal boundaries.

Analytical solution of fractional oscillation equation with two Caputo fractional derivatives

Analytical solution of initial value problem for the fractional oscillation equation with two Caputo fractional derivatives , where the coefficients and orders satisfy and , is investigated by using the Laplace transform and complex inverse integral method on the principal Riemann surface. It is proved by using the argument principle that the characteristic equation has a pair of conjugated simple complex roots with a negative real part on the principal Riemann surface under the assumption that and are not both integers. Then three fundamental solutions, the unit impulse response, the unit initial displacement response, and the unit initial rate response, are derived analytically. Each of these solutions is expressed into a superposition of a classical damped oscillation decaying exponentially and a real Laplace integration decaying in a negative power law. Finally, the asymptotic behaviors of these analytical solutions for sufficiently large are determined as monotonous decays in a power of negative exponent.

Analysis of cryopreservation media thermophysical characteristics after ultra-rapid cooling through differential scanning calorimetry

Cryoprotective agents play a critical role in minimizing cell damage caused by ice formation during cryopreservation. However, high concentrations of CPAs are toxic to cells and tissues. Required concentrations of CPAs can be reduced by utilizing higher cooling and warming rates, but insight into the thermophysical properties of biological solutions in the vitrification method is necessary for the development of cryopreservation protocols. Most studies on thermophysical properties under ultra-rapid cooling conditions have been qualitatively based on visualization. Differential scanning calorimetry methods are ideal for studying the behavior of biomaterials in various freezing conditions quantitatively and accurately, though previous studies have been predominantly restricted to slower cooling rates. Here, we developed an ultra-rapid cooling method for DSC that can achieve minimal cooling rates exceeding 2000 °C/min. We investigated the thermophysical vitrification behavior of ternary solutions of phosphate buffer saline (1X), dimethyl sulfoxide or glycerol and ice blocking polymers (X-1000 or Z-1000). We quantified the impact of solute concentration on ice crystal formation during rapid cooling. Our findings support the expectation that increasing the solute concentration reduces the amount of ice formation, including devitrification. Devitrification increases from 0 % to 40 % (v/v) Me2SO and then reduces significantly. The relative amounts of devitrification to the total ice formation are 0 %, 60 %, 0 % in 20 %, 40 %, 60 % (v/v) Me2SO, and 2 %, 48 %, 49 % in 20 %, 40 %, 60 % (v/v) glycerol, respectively. The results suggest that at low concentrations, such as below 20 % (v/v) for Me2SO or glycerol, increasing the warming rate after ultra-rapid freezing is not essential to eliminate devitrification. Furthermore, ice blocking polymers do not reduce ice formation substantially and cannot eliminate devitrification under ultra-rapid cooling conditions. In conclusion, our results provide insights into the impact of solute concentration on ice formation and devitrification during rapid cooling, which can be practical for optimizing cryopreservation protocols.

Oscillatory behavior of solutions of second-order non-linear differential equations with mixed non-linear neutral terms

This study primarily seeks to expand upon these developments by encompassing neutral differential equations of mixed type, incorporating both delay and advanced terms, particularly in the case of the canonical operator. The presented results are derived from the application of the comparison method, Riccati transformation, and integral averaging technique. These methodologies lead to substantial improvements and extensions of existing results found in the literature. Additionally, illustrative examples are provided to demonstrate the practical implications of the developed criteria.

The ion-activated attractive patchy particle model and its application to the liquid-vapor phase transitions.

Patchy particles are an intriguing subject of study and indeed a model system in the field of soft matter physics. In recent years, patchy particle models have been applied to describe a wide variety of systems, including colloidal crystals, macromolecular interactions, liquid crystals, and nanoparticle assemblies. Given the importance of the topic, rationalizing and capturing the basic features of these models is crucial to their correct application in specific systems. In this study, we extend the ion-activated attractive patchy particles model previously employed to elucidate the phase behavior of protein solutions in the presence of trivalent salts. Our extension incorporates the effect of repulsion between unoccupied and occupied binding sites, depicted as patches. Furthermore, we examine the influence of model parameters on the liquid-vapor coexistence region within the phase diagram, employing numerical methods. A deeper understanding of this model will facilitate a better comprehension of the effects observed in experiments.

Asymptotic behavior of Riemann solutions for the one-dimensional mean-field games in conservative form with the logarithmic coupling term

Construction of Riemann solutions for a hyperbolic system in conservative form arising from the one-dimensional mean-field games with the quadratic Hamiltonian and the logarithmic coupling term are provided in detail. Moreover, the delta shock formation is concretely analyzed from the limit of double-shock-solution as well as the emergence of vacuum state is also specifically discussed from the limit of double-rarefaction-solution when the coupling coefficient drops to zero. Accordingly, the remarkable cavitation and concentration phenomena can be closely observed and explored. Additionally, the numerical experiments are also presented in correspondence to authenticate the theoretical analysis results.

Actinium chelation and crystallization in a macromolecular scaffold

Targeted alpha therapy (TAT) pairs the specificity of antigen targeting with the lethality of alpha particles to eradicate cancerous cells. Actinium-225 [225Ac; t1/2 = 9.920(3) days] is an alpha-emitting radioisotope driving the next generation of TAT radiopharmaceuticals. Despite promising clinical results, a fundamental understanding of Ac coordination chemistry lags behind the rest of the Periodic Table due to its limited availability, lack of stable isotopes, and inadequate systems poised to probe the chemical behavior of this radionuclide. In this work, we demonstrate a platform that combines an 8-coordinate synthetic ligand and a mammalian protein to characterize the solution and solid-state behavior of the longest-lived Ac isotope, 227Ac [t1/2 = 21.772(3) years]. We expect these results to direct renewed efforts for 225Ac-TAT development, aid in understanding Ac coordination behavior relative to other +3 lanthanides and actinides, and more broadly inform this element’s position on the Periodic Table.

Phase separation behavior and CO2 absorption kinetic analysis of DETA/DEA/DMAC biphasic absorbent

Lower regeneration energy and superior cyclic capacity have enabled biphasic absorbents great potential in the area of flue gas CO2capture. The liquid film mass transfer coefficient(kL) is a vital parameter in the development of absorbents with efficient CO2 absorption mass transfer performance, while the phase separation behavior of biphasic solutions could be an essential factor for the absorption mass transfer and the stability of absorber. However, systemic kinetic research towards biphasic absorbents, especially the impact of phase separation behavior, is limited. In this study, a typical amide-based biphasic absorbent diethylenetriamine(DETA)/diethanolamine(DEA)/N, N-dimethylacetamide(DMAC) which has achieved great reduction in regeneration energy, was selected as the subject of kinetic investigation in a wetted wall column. The CO2 overall mass transfer coefficient(KG) of DETA/DEA/DMAC exceeded other biphasic solvents, blended amine solution, and 40% K2CO3 solution, with 3 times that of 40% K2CO3 solution. Moreover, various operational conditions including absorption temperature, gas flow rate, and water content of solution were taken into account to build a multiple-condition kinetic mechanism to offer guidance for biphasic absorbents. Furthermore, phase separation behavior was revealed as the main blame for the deterioration in the liquid film chemical mass transfer process of biphasic solvents in the CO2 absorption process, resulting in the kL of DETA/DEA/DMAC before phase separation decreased by 75.3% at the phase separation stage. Therefore, it is crucial to ensure that the CO2 loading of the solution entering absorber is lower than the phase separation point in applications. After phase separation, DETA/DEA/DMAC split into the organic and aqueous phases, the kL of the aqueous phase gradually exceeded that of the organic phase as CO2 loading increased for its higher chemical enhancement factor(E).

Dynamics of a delayed nonlocal reaction–diffusion heroin epidemic model in a heterogenous environment

To study the consumption of heroin in a heterogeneous environment, we propose and analyze a spatiotemporal model with a distributed delay. Using the spectral theory, we determine the basic reproduction number , which serves a threshold role. If , then the addiction‐free steady state is globally asymptotically stable while if , then there is at least one addictive steady state. Moreover, when , if one of the dispersal coefficients is zero, then there is only one addictive steady state, and it is globally asymptotically stable; if both diffusions of susceptible and addicted individuals are present, we cannot identify the temporal behavior of solutions, and hence, we study the asymptotic profile of addictive steady states when one of the dispersal coefficients tend to zero.

Gold-Thiolate Nanocluster Dynamics and Intercluster Reactions Enabled by a Machine Learned Interatomic Potential.

Monolayer protected metal clusters comprise a rich class of molecular systems and are promising candidate materials for a variety of applications. While a growing number of protected nanoclusters have been synthesized and characterized in crystalline forms, their dynamical behavior in solution, including prenucleation cluster formation, is not well understood due to limitations both in characterization and first-principles modeling techniques. Recent advancements in machine-learned interatomic potentials are rapidly enabling the study of complex interactions such as dynamical behavior and reactivity on the nanoscale. Here, we develop an Au-S-C-H atomic cluster expansion (ACE) interatomic potential for efficient and accurate molecular dynamics simulations of thiolate-protected gold nanoclusters (Aun(SCH3)m). Trained on more than 30,000 density functional theory calculations of gold nanoclusters, the interatomic potential exhibits ab initio level accuracy in energies and forces and replicates nanocluster dynamics including thermal vibration and chiral inversion. Long dynamics simulations (up to 0.1 μs time scale) reveal a mechanism explaining the thermal instability of neutral Au25(SR)18 clusters. Specifically, we observe multiple stages of isomerization of the Au25(SR)18 cluster, including a chiral isomer. Additionally, we simulate coalescence of two Au25(SR)18 clusters and observe series of clusters where the formation mechanisms are critically mediated by ligand exchange in the form of [Au-S]n rings.

Heat equation on the hypergraph containing vertices with given data

This paper is concerned with a multivalued ordinary differential equation governed by the hypergraph Laplacian, which describes the diffusion of “heat” or “particles” on the vertices of hypergraph. We consider the case where the heat on several vertices is manipulated internally by the observer, namely, are fixed by some given functions. This situation can be reduced to a nonlinear evolution equation associated with a time-dependent subdifferential operator, whose solvability has been investigated in numerous previous researches. In this paper, we give an alternative proof of the solvability in order to avoid some complicated calculations arising from the chain rule for the time-dependent subdifferential. As for results which cannot be assured by the known abstract theory, we also discuss the continuous dependence of solution on the given data and the time-global behavior of solution.

Long‐time asymptotics of solution for the fifth‐order modified KdV equation in the presence of discrete spectrum

AbstractWe investigate the Cauchy problem of an integrable focusing fifth‐order modified Korteweg–de Vries (KdV) equation, which contains the fifth‐order dispersion and relevant higher order nonlinear terms. The long‐time asymptotics of solution is established in the case of initial conditions that lie in some low regularity weighted Sobolev spaces and allow for the presence of discrete spectrum. Our method is based on a generalization of the nonlinear steepest descent method of Deift and Zhou. We show that the solution decomposes in the long time into three main regions: (i) an expanding oscillatory region where solitons and breathers travel with positive velocities, the leading order term has the form of a multisoliton/breather and soliton/breather–radiation interactions; (ii) a Painlevé region, which does not have traveling solitons and breathers, the asymptotics can be characterized with the solution of a fourth‐order Painlevé II equation; (iii) a region of breathers traveling with negative velocities. Employing a global approximation via PDE techniques, the asymptotic behavior of solution is extended to lower regularity spaces with weights.

Two-Dimensional Cu-Based MOF for Selective Staining of the Cellular Nucleus through Fluorescence Imaging and Selective Sorption of Dye Molecules in Aqueous Medium.

A two-dimensional copper-based metal-organic framework, [Cu(C23H14O6)(C10H8N2)2]·H2O·DMSO, 1, was synthesized using pamoic acid (C23H16O6) and 4,4'-bipyridine (C10H8N2) as an organic ligand and Cu(II) as a metal ion. Single-crystal structure X-ray diffraction studies of the as-synthesized compound showed a two- dimensional structure with free hydroxyl groups. Upon excitation at 370 nm, the aqueous dispersion of [Cu(C23H14O6)(C10H8N2)2]·H2O·DMSO, 1, showed emission centered at 525 nm resulting from the intraligand energy transfer. Fluorescence microscopic experiments using a human epithelioid cervix carcinoma HeLa cell line were carried out, clearly showing that our compound selectively stained the cellular nucleus. To utilize the porous nature of [Cu(C23H14O6)(C10H8N2)2]·H2O·DMSO, 1, its dye sorption behavior in aqueous solution was determined, and a high affinity for methylene blue (MB) dye was confirmed. Our synthesized compound sorbed 88% MB dye with an initial concentration of 32 mg L-1, and its sorption capacity for MB was found to be 29.79 mg g-1. The possible mechanism of the dye sorption behavior was discussed in terms of the size and charge of dye molecules with respect to molecular-level interactions between the framework and the dye molecules.

Multicomponent nonlinear fractional Schrödinger equation: On the study of optical wave propagation in the fiber optics

In this article, we investigate the soliton wave dynamics of the fractional three-component coupled nonlinear Schrödinger equation. This equation is considered as a fundamental tool for describing the behavior of optical pulses in optical fibers. There is increasing interest in studying these equations as they can be used to explain a wide range of complex physical phenomena in various scientific and engineering fields, including nonlinear fiber optics, electromagnetic field waves, and signal processing through optical fibers. In order to obtain the required solutions, the first step is to apply the complex wave transformations with β-fractional derivative to obtain the nonlinear ordinary differential equations of the governing model. Furthermore, by applying the novel integration methods known as generalized Arnous method and multivariate generalized exponential rational integral function approach, different type of soliton solutions are extracted. Different sets and values of the physical parameters are used to study the optical soliton solutions of the studied system. Based on a comparative analysis of our results with existing techniques, this study concludes that our proposed solutions are novel. The results described in this work are able to enhance the nonlinear dynamical behavior of a given system and confirm the effectiveness of the methods used. Furthermore, the different graphs are sketched to visualize the solutions behavior with various parametric values. It is anticipated that obtained solutions will be significant in the study of wave propagation and other related fields.

Ab initio investigation of the geometrical behavior in solution and electronic structure of the anion complexes [bis(1,3-dithiole-2-thione-4,5-dithiolate)M], for M = Bi(III), Sb(III), and Zn(II).

1,3-Dithiole-2-thione-4,5-dithiolate (dmit) ligands are known for their conductive and optical properties. Dmit compounds have been assessed for use in sensor devices, information storage, spintronics, and optical material applications. Associations with various metallic centers endow dmit complexes with magnetic, optical, conductive, and antioxidant properties. Optical doping can facilitate the fabrication of magnetic conductor materials from ground-state nonmagnetic cations. While most studied complexes involve transition-metal centers due to their diverse chemistry, compounds with representative elements are less explored in the literature. This study investigated the structural and electronic properties of bisdmit complexes with representative Bi(III), Sb(III), and Zn(II) cations. AIMD calculations revealed two new geometries for Bi(III) and Zn(II) complexes, diverging from the isolated geometry typically used in quantum chemical calculations. The coordination of acetonitrile molecules to the cationic centers of the complexes resulted in unstable structures, while the dimerization of the complexes was stable. SA-CASSCF/NEVPT2 calculations were applied to the structures of the isolated complexes and stable dimers, confirming the multireference character of the electronic structure of the three systems and the multiconfigurational character of the Bi(III) complex. The electronic spectra simulated by the STEOM-DLPNO-CCSD calculations accurately reproduced the experimental UV‒Vis spectra indicating the participation of the isolated Bi(III) dmit complex and its dimeric form in solution. AIMD calculations of the dmit salts were conducted using the GFN2-xTB method with 60 explicit acetonitrile molecules as the solvent at 300K for a total simulation time of 50.0ps, with printing intervals of 0.5fs. The final geometries were optimized employing the PBEh-3c compound method, incorporating implicit conductor-like polarizable continuum model (CPCM) solvation for acetonitrile. Local energy decomposition (LED) analysis at the DLPNO-CCSD(T)/Def2-TZVP level of theory was utilized to investigate the stability of the complex geometries identified by AIMD. The electronic structures of the complexes were assessed using the SA-CASSCF/NEVPT2/Def2-TZVP method to confirm the multiconfigurational and multireference nature of their electronic structures. Electronic spectra were analyzed using the STEOM-DLPNO-CCSD/Def2-TZVP method, with CPCM used to simulate an acetonitrile medium.

Shear thickening behaviour of polyborosiloxane

Polyborosiloxane (PBS) is often referred to as a “shear thickening/stiffening gel” or “dilatant compound”, sometimes actually meaning an increase in modulus with frequency/strain rate rather than the rheological definition of “dilatant compound”, i.e. an increase in viscosity with shear rate. The shear behaviour of bulk PBS and PBS solution has been studied here by steady shear experiments, and it is observed that PBS exhibits shear thickening behaviour only under certain conditions. The shear behaviour of bulk PBS depends on the degree of reaction of the PBS (i.e. the content of B in the PBS). For PBS solution, the shear behaviour is influenced by the concentration of the solution and the type of solvent (with or without oxygen atom in the solvent). The shear behaviour of PBS systems is related to shear induced structural changes, where the formation of new elastically active B:O dynamic dative bonds (interchain cross-linking) contributes to shear thickening.

Physicochemical and Spectroscopic Characterization of Glycogen and Glycogen Phosphorylase b Complexes

Glycogen is a natural polysaccharide used as an energy storage macromolecule. The role of glycogen metabolism in type 2 diabetes mellitus has been under investigation for several years, along with its implication in cancer and cardiovascular and neurodegenerative diseases. Previous studies using pig liver glycogen with rabbit muscle glycogen phosphorylase (RMGPb), which catalyzes the first step of glycogen degradation to glucose-1-phosphate, showed that the surface of an average glycogen molecule is covered by a total of 20 RMGPb dimeric molecules. In this work, we selected oyster glycogen (Glyc) to investigate its interaction with RMGPb by employing biophysical techniques. Dynamic, static, and electrophoretic light scattering were used to investigate the solution behaviors and structures of both the Glyc molecule itself and the formed complexes between Glyc and GPb at different mixing ratios. It was established that the interaction between oyster Glyc and RMGPb is similar to that previously reported for pig liver glycogen. Moreover, the structure of the complexed GPb was monitored by fluorescence and FTIR spectroscopy.

Multi-bump solutions to Kirchhoff type equations in the plane with the steep potential well vanishing at infinity

In this paper, we study the following Kirchhoff type equation with a steep potential well vanishing at infinity:−(a+b∫R2|∇u|2dx)Δu+(h(x)+μV(x))u=K(x)f(u)inR2, where a,b>0 are constants, μ>0 is a parameter, V decays to zero at infinity as |x|−γ with γ∈(0,2] and intV−1(0) possesses multiple disjoint bounded components. We prove the existence of multi-bump solutions for μ>0 large enough and the concentration behavior of multi-bump solutions as μ→+∞.

Investigation on ion concentration of pore water in compacted bentonite after infiltrated by salt solutions

The behavior of salt solutions infiltrated into compacted bentonite was investigated in this study, with particular attention paid to the ion concentration in the pore water, in order to improve the understanding of the bentonite behavior in geological disposal projects. A Japanese bentonite, Kunigel V1 (K_V1), was used to prepare specimens with a thickness of 2 mm and an initial dry density of 1.4 to 1.7 Mg/m3. For each density case, salt solutions (NaCl, KCl, and CaCl2) of different amounts (0 to 2 mol/L) were supplied to the specimens. After infiltration, the basal spacing (d001) and exchangeable cations of the montmorillonite in the bentonite and the leached cations from the bentonite were measured. Based on the test results, the ion concentration in the interlayer pore water of the montmorillonite or the interparticle pore water was discussed. The findings indicated that the infiltration capacities of the various salt solutions into the compacted K_V1 bentonite were in the order of KCl > CaCl2 > NaCl. The K_V1 specimen with the highest initial dry density exhibited the strongest resistance to salt solution infiltration. After the infiltration of the NaCl solution into the compacted K_V1 bentonite, the increased sodium ions mainly remained in the interparticle pores, leading to an increase in the sodium ion concentration in the interparticle pore water. During the infiltration of the KCl and CaCl2 solutions into the compacted K_V1 bentonite, the infiltrated potassium ions in the case of KC1 and the calcium ions in the case of CaCl2 tended to penetrate the interlayer pore preferentially, thereby displacing the exchangeable sodium ions. After most of the exchangeable sodium ions that had initially existed in the montmorillonite had been replaced, the infiltrated potassium or calcium ions remained in the interparticle pores.