Molecular simulation of solid–solid phase transitions

Applications of dl_poly to solid–solid phase transitions are reviewed, with particular attention to how details of the mechanisms of the transitions may be extracted from molecular dynamics simulations. Two examples in molecular crystals are discussed: the order–disorder transition of p-terphenyl initiated at around 200 K by the unlocking of ring flipping; and the rotator phases of n-alkanes with around 20 carbon atoms per chain, showing distinct molecular mechanisms in the dynamics just below the melting points of odd and even chains. Covalent-ionic materials are represented by an application to an aluminophophate molecular sieve, AlPO₄-5.     

Physical properties of detergent-based aqueous two–phase systems

The physical behavior of the binary phase systems of the non-ionic polyoxyethylene detergent Agrimul NRE 1205 and water was investigated. This technical detergent can be used for the large-scale recovery of biomolecules in detergent based aqueous two-phase systems. The phase diagram was determined. It shows significant and unexpected differences to highly purified detergents. Very similar to neat detergents the phase diagram can be influenced by auxiliary chemicals thus shifting the entire phase diagram in general to lower temperatures. This was demonstrated by lowering the cloud-point by various additions. The concentration factor, as an important parameter of a first capture step in purification was investigated and modeled. Auxiliary chemicals, temperature change and change in detergent concentration also influence the viscosity and density of the phases. These experimental data are shown. They can help to explain the separation behavior of proteins. In large-scale separations aqueous two-phase systems are separated using disc-stack centrifuges. It is demonstrated that this is not a feasible method for detergent-based aqueous two-phase extraction and the physical reason is presented. This revised version was published online in July 2006 with corrections to the Cover Date.     

Corresponding states vapour–liquid phase equilibria of confined square–well fluid

Corresponding states vapour–liquid phase equilibria of confined square-well fluid are studied by means of grand-canonical transition-matrix Monte Carlo simulation and histogram reweighting method. In this study, square-well fluid is considered under hard and attractive slit pore confinements ranging from 1.5 to 40 molecular diameters. Corresponding states vapour–liquid phase coexistence envelopes display insignificant effect of wall?fluid interaction for slit pore confinements ranging from 1.5 to 3 molecular diameters. On the other hand, significant effect of wall?fluid interaction on the corresponding state coexistence envelope is observed for slit pore confinements ranging from 4 to 40 molecular diameters. Moreover, at a given slit width, shrinking in corresponding state coexistence envelope is observed with increase in the wall?fluid interaction. However, in the larger slit pore width of 30 to 40 molecular diameters, shrinking in the corresponding state vapour–liquid coexistence envelopes become indifferent with the stronger wall?fluid interactions studied in this work. Structural behaviour of coexisting phases in slit pores are also investigated through local density profiles, to understand the overall behaviour of corresponding states coexistence envelopes. Fluctuating positive and negative deviations in the corresponding state spreading pressure with respect to corresponding bulk value is observed for studied wall?fluid interactions and slit pore confinements.     

Comprehensive analysis of lncRNA–miRNA–mRNA during proliferative phase of rat liver regeneration

This study aims to reveal the regulatory mechanism of lncRNAs–miRNAs–mRNAs network during the proliferative phase of liver regeneration (LR). High-throughput sequencing technology was performed, and a total of 1,738 differentially expressed lncRNAs (DE lncRNAs), 167 known differentially expressed miRNAs (DE miRNAs), and 2,727 differentially expressed mRNAs were identified. Then, the target DE lncRNAs and DE mRNAs regulated by the same miRNAs were screened and a ceRNA regulatory network containing 32 miRNAs, 107 lncRNAs, and 270 mRNAs was constructed. Insulin signaling pathway, pyrimidine metabolism, axon guidance, carbohydrate digestion and absorption, and pyruvate metabolism were significantly enriched in the network. Through literature review and the regulatory relationship between lncRNAs and miRNAs, nine core lncRNAs were identified, which might play important roles during the proliferative phase of rat LR. This study analyzed lncRNA–miRNA–mRNA regulatory network for the first time during the proliferative phase of rat LR, providing clues for exploring the mechanism of LR and the treatment of liver diseases.     

Vapour–liquid phase equilibria of simple fluids confined in patterned slit pores

We present the influence of surface heterogeneity on the vapour–liquid phase behaviour of square-well fluids in slit pores using grand-canonical transition-matrix Monte Carlo simulations along with the histogram-reweighting method. Properties such as phase coexistence envelopes, critical properties and local density profiles of the confined SW fluid are reported for chemically and physically patterned slit surfaces. It is observed that in the chemically patterned pores, fluid–fluid and surface attraction parameters along with the width of attractive and inert stripes play fundamentally different roles in the phase coexistence and critical properties. On the other hand, pillar gap and height significantly affect the vapour–liquid equilibria in the physically patterned slit pores. We also present the effect of chemically and physically patterned slit surfaces on the spreading pressure.     

Cyclic dipeptide-based small molecules modulate zinc-mediated liquid–liquid phase separation of tau

Liquid–liquid phase separation (LLPS) is a complex physicochemical phenomenon mediated by multivalent transient weak interactions among macromolecules like polymers, proteins, and nucleic acids. It has implications in cellular physiology and disease conditions like cancer and neurodegenerative disorders. Many proteins associated with neurodegenerative disorders like RNA binding protein FUS (FUsed in Sarcoma), alpha-synuclein (α-Syn), TAR DNA binding protein 43 (TDP-43), and tau are shown to undergo LLPS. Recently, the tau protein responsible for Alzheimer's disease (AD) and other tauopathies is shown to phase separate into condensates in vitro and in vivo. The diverse noncovalent interactions among the biomolecules dictate the complex LLPS phenomenon. There are limited chemical tools to modulate protein LLPS which has therapeutic potential for neurodegenerative disorders. We have rationally designed cyclic dipeptide (CDP)-based small-molecule modulators (SMMs) by integrating multiple chemical groups that offer diverse chemical interactions to modulate tau LLPS. Among them, compound 1c effectively inhibits and dissolves Zn-mediated tau LLPS condensates. The SMM also inhibits tau condensate-to-fibril transition (tau aggregation through LLPS). This approach of designing SMMs of LLPS establishes a novel platform that has potential implication for the development of therapeutics for neurodegenerative disorders.     

Biophysics of endocytic vesicle formation: A focus on liquid–liquid phase separation

Endocytosis is a fine-tuned mechanism of cellular communication through which cells internalize molecules on the plasma membrane, such as receptors and their bound ligands. Through receptor clustering in endocytic pits, recruitment of active receptors to different endocytic routes and their trafficking towards different fates, endocytosis modulates cell signaling and ultimately leads to a variety of biological responses. Many studies have focused their attention on specialized endocytic mechanisms depending on the nature of the internalizing cargo and cellular context, distinct sets of coat proteins, endocytic adaptors and membrane lipids. Here, we review recent advances in our understanding of the principles underlying endocytic vesicle formation, integrating both biochemical and biophysical factors, with a particular focus on intrinsically disordered regions (IDRs) creating weakly interconnected protein networks assembled through liquid–liquid phase separation (LLPS) and driving membrane bending especially in clathrin-mediated endocytosis (CME). We finally discuss how these properties impinge on receptor fate and signaling.     

Analysis of functional brain connections for positive–negative emotions using phase locking value

In this study, we investigate the brain networks during positive and negative emotions for different types of stimulus (audio only, video only and audio + video) in \(\alpha , \beta\), and \(\gamma\) bands in terms of phase locking value, a nonlinear method to study functional connectivity. Results show notable hemispheric lateralization as phase synchronization values between channels are significant and high in right hemisphere for all emotions. Left frontal electrodes are also found to have control over emotion in terms of functional connectivity. Besides significant inter-hemisphere phase locking values are observed between left and right frontal regions, specifically between left anterior frontal and right mid-frontal, inferior-frontal and anterior frontal regions; and also between left and right mid frontal regions. ANOVA analysis for stimulus types show that stimulus types are not separable for emotions having high valence. PLV values are significantly different only for negative emotions or neutral emotions between audio only/video only and audio only/audio + video stimuli. Finding no significant difference between video only and audio + video stimuli is interesting and might be interpreted as that video content is the most effective part of a stimulus.     

Thermal and pressure-induced martensitic phase transformations in a Ni–Al alloy modelled by Sutton–Chen embedded atom method

The Ni–Al alloys which exhibit the thermoelastic martensitic phase transformations in the composition range from 60 to 65 atomic percentage (at.%) of Ni are widely used in the high technology applications. In this study, both thermal and pressure-induced phase transformations in Ni-37.5 at.%Al alloy model were investigated by a molecular dynamics (MD) method. Physical interactions between atoms in the alloy system were modelled using the Sutton–Chen version of the embedded atom method based on many-body interactions. The potential parameters for cross interactions between Ni and Al atoms were estimated by optimising the results obtained from the MD simulations, taking into account the experimental data including the crystal lattice properties of the model alloy in high temperature phase.     

Chlorophyll a fluorescence induction: a personal perspective of the thermal phase, the J–I–P rise

The fast (up to 1?s) chlorophyll (Chl) a fluorescence induction (FI) curve, measured under saturating continuous light, has a photochemical phase, the O-J rise, related mainly to the reduction of Q(A), the primary electron acceptor plastoquinone of Photosystem II (PSII); here, the fluorescence rise depends strongly on the number of photons absorbed. This is followed by a thermal phase, the J-I-P rise, which disappears at subfreezing temperatures. According to the mainstream interpretation of the fast FI, the variable fluorescence originates from PSII antenna, and the oxidized Q(A) is the most important quencher influencing the O-J-I-P curve. As the reaction centers of PSII are gradually closed by the photochemical reduction of Q(A), Chl fluorescence, F, rises from the O level (the minimal level) to the P level (the peak); yet, the relationship between F and [Q(A) (-)] is not linear, due to the presence of other quenchers and modifiers. Several alternative theories have been proposed, which give different interpretations of the O-J-I-P transient. The main idea in these alternative theories is that in saturating light, Q(A) is almost completely reduced already at the end of the photochemical phase O-J, but the fluorescence yield is lower than its maximum value due to the presence of either a second quencher besides Q(A), or there is an another process quenching the fluorescence; in the second quencher hypothesis, this quencher is consumed (or the process of quenching the fluorescence is reversed) during the thermal phase J-I-P. In this review, we discuss these theories. Based on our critical examination, that includes pros and cons of each theory, as well mathematical modeling, we conclude that the mainstream interpretation of the O-J-I-P transient is the most credible one, as none of the alternative ideas provide adequate explanation or experimental proof for the almost complete reduction of Q(A) at the end of the O-J phase, and for the origin of the fluorescence rise during the thermal phase. However, we suggest that some of the factors influencing the fluorescence yield that have been proposed in these newer theories, as e.g., the membrane potential ΔΨ, as suggested by Vredenberg and his associates, can potentially contribute to modulate the O-J-I-P transient in parallel with the reduction of Q(A), through changes at the PSII antenna and/or at the reaction center, or, possibly, through the control of the oxidation-reduction of the PQ-pool, including proton transfer into the lumen, as suggested by Rubin and his associates. We present in this review our personal perspective mainly on our understanding of the thermal phase, the J-I-P rise during Chl a FI in plants and algae.     

GPU-accelerated replica exchange molecular simulation on solid–liquid phase transition study of Lennard-Jones fluids

Determining the solid–liquid phase transition point by conventional molecular dynamics (MD) simulations is difficult because of the tendency of the system to get trapped in local minimum energy states at low temperatures and hysteresis during cooling and heating cycles. The replica exchange method, used in performing many MD simulations of the system at different temperature conditions simultaneously and performs exchanges of these temperatures at certain intervals, has been introduced as a tool to overcome this local-minimum problem. However, around the phase transition temperature, a greater number of different temperatures are required to adequately find the phase transition point. In addition, the number of different temperature values increases when treating larger systems resulting in huge computation times. We propose a computational acceleration of the replica exchange MD simulation on graphics processing units (GPUs) in studying first-order solid–liquid phase transitions of Lennard-Jones (LJ) fluids. The phase transition temperature for a 108-atom LJ fluid has been calculated to validate our new code. The result corresponds with that of a previous study using multicanonical ensemble. The computational speed is measured for various GPU-cluster sizes. A peak performance of 196.3 GFlops with one GPU and 8.13 TFlops with 64 GPUs is achieved.     

Photodynamic therapy–generated cancer vaccine elicits acute phase and hormonal response in treated mice

Photodynamic therapy (PDT)-generated cancer vaccines have shown promising results in preclinical studies and are being introduced in the clinics. Using an SCCVII mouse squamous cell carcinoma-based whole-cell autologous PDT vaccine model developed in our previous work, we have examined systemic effects in vaccinated mice that could be related to the induction of acute phase response. The upregulation of gene encoding serum amyloid P component (prototypic mouse acute phase reactant) was detected in the liver and to a lesser degree in the tumor of vaccinated mice at 24 h post-PDT vaccine treatment. A strong upregulation of gene for heat shock protein 70 was found in both the liver and tumor of mice at 4 h after their PDT vaccine treatment. Changes in the expression of genes for glucocorticoid-induced leucine zipper and serum- and glucocorticoid-regulated kinase 1 that are highly responsive to glucocorticoid modulation were uncovered in both the tumor and liver of vaccinated mice. A rise in the levels of serum corticosterone was detected in mice at 24 h after PDT vaccine treatment. The results indicate that a sudden appearance of a large number of PDT vaccine cells elicits host responses for securing their optimized clearance, which in addition to producing seminal acute phase reactants includes the engagement of glucocorticoid hormones. It is becoming increasingly clear that a consummate execution of this process of PDT vaccine cell removal is critical for tumor antigen recognition and the attainment of potent antitumor immune response.     

Ordering of p–n-alkoxybenzoic acids at phase transition temperatures: a comparative computational analysis

A comparative analysis of molecular ordering of nematogenic p-n-alkoxybenzoic acids has been carried out with respect to translatory and orientational motions for the acids with seven (7OBAC), eight (8OBAC), nine (9OBAC) and 10 (10OBAC) carbon atoms in the alkyl chain. The CNDO/2 method has been used to compute the net atomic charge and dipole moment components at each atomic center. Modified Rayleigh-Schrodinger perturbation theory with multicentered-multipole expansion method has been used to evaluate long-range intermolecular interactions while a '6-exp' potential function has been assumed for short-range interactions. The total interaction-energy values obtained by these computations were used to calculate the probability of each configuration at the phase-transition temperature using the Maxwell-Boltzmann formula. The flexibility of various configurations has been studied in terms of variation of probability due to small departures from the most probable configuration. A comparative picture of molecular parameters like total energy, binding energy and total dipole moment has been given. An attempt has been made to explain the nematogenicity of these acids in terms of their relative order with the molecular parameter introduced in this paper.     

Chiral amorphous metal–organic polyhedra used as the stationary phase for high-resolution gas chromatography separations

Herein, we describe a new chiral amorphous metal–organic polyhedra used as the stationary phase for high-resolution gas chromatography (GC). The chiral stationary phase was coated onto a capillary column via a dynamic coating process and investigated for a variety of compounds. The experimental results showed that the chiral stationary phase exhibits good selectivity for linear alkanes, linear alcohols, polycyclic aromatic hydrocarbons, isomers, and chiral compounds. In addition, the column has the advantages of high column efficiency and short analysis time. The present work indicated that amorphous metal–organic polyhedra have great potential for application as a new type of stationary phase for GC.     

Average phase difference theory and 1∶1 phase entrainment in interlimb coordination

The dynamics of coupled biological oscillators can be modeled by averaging the effects of coupling over each oscillatory cycle so that the coupling depends on the phase difference between the two oscillators and not on their specific states. Average phase difference theory claims that mode locking phenomena can be predicted by the average effects of the coupling influences. As a starting point for both empirical and theoretical investigations, Rand et al. (1988) have proposed d/dt= — K sin ), with phase-locked solutions =arcsin( /K), where is the difference between the uncoupled frequencies and K is the coupling strength. Phase-locking was evaluated in three experiments using an interlimb coordination paradigm in which a person oscillates hand-held pendulums. was controlled through length differences in the left and right pendulums. The coupled frequency _c was varied by a metronome, and scaled to the eigenfrequency _v of the coupled system K was assumed to vary inversely with _c. The results indicate that: (1) and K contribute multiplicatively to (2) =0 or = regardless of K when =0; (3) 0 or regardless of when K is large (relative to ); (4) results (1) to (3) hold identically for both in phase and antiphase coordination. The results also indicate that the relevant frequency is _c/_v rather than _c. Discussion high-lighted the significance of confirming =arcsin(/K) for more general treatments of phase-locking, such as circle map dynamics, and for the 11 phase-entrainment which characterizes biological movement systems.     

How does acyl chain length affect thermotropic phase behavior of saturated diacylphosphatidylcholine–cholesterol binary bilayers?

Thermotropic phase behavior of diacylphosphatidylcholine (CnPC)–cholesterol binary bilayers (n = 14–16) was examined by fluorescence spectroscopy using 6-propionyl-2-(dimethylamino)naphthalene (Prodan) and differential scanning calorimetry. The former technique can detect structural changes of the bilayer in response to the changes in polarity around Prodan molecules partitioned in a relatively hydrophilic region of the bilayer, while the latter is sensitive to the conformational changes of the acyl chains. On the basis of the data from both techniques, we propose possible temperature T–cholesterol composition X_ch phase diagrams for these binary bilayers. A notable feature of our phase diagrams, including our previous results for diheptadecanoylphosphatidylcholine (C17PC) and distearoylphosphatidylcholine (C18PC), is that there is a peritectic-like point around X_ch = 0.15, which can be interpreted as indicating the formation of a 1:6-complex of cholesterol and CnPCs within the binary bilayer irrespective of the acyl chain length. We could give a reasonable explanation for such complex formation using the modified superlattice view. Our results also showed that the X_ch value of the abolition of the main transition is almost constant for n = 14–17 (ca. 0.33), while it increases to ca. 0.50 for n = 18. By contrast, a biphasic n-dependence of X_ch was observed for the abolition of the pretransition, suggesting that there are at least two antagonistic n-dependent factors. We speculate that this could be explained by the enhancement of the van der Waals interaction with increases in n and the weakening of the repulsion between the neighboring headgroups with decreases in n.