拥挤剂粒子形状对大分子链成环动力学的影响

Using 3D Langevin dynamics simulations,we investigate the effects of the shape of crowders on the dynamics of a polymer chain closure.The chain closure in spherical crowders is dominated by the increased medium viscosity so that it gets slower with the increasing volume fraction of crowders.By contrast,the dynamics of chain closure becomes very complicated with increasing volume fraction of crowders in spherocylindrical crowders.Notably,the mean closure time is found to have a dramatic decrease at a range of volume fraction of crowders 0.36-0.44.We then elucidate that an isotropic to nematic transition of spherocylindrical crowders at this range of volume fraction of crowders is responsible for the unexpected dramatic decrease in the mean closure time.     

Simple Model Study of Phase Transition Properties of Isolated and Aggregated Protein

We investigate the phase transition properties of isolated and aggregated protein by exhaustive numerical study in the confined conformation space with maximally compact lattice model. The study within the confined conformation space shows some general folding properties. Various sequences show different folding properties: two-state folding, three-state folding and prion-like folding behavior. We find that the aggregated protein holds a more evident transition than isolated one and the transition temperature is generally lower than that in isolated case.     

Shape transition of semi-flexible macromolecules confined in channel and cavity

Stiff macromolecules entrapped in channels or in spherical cavities undergo a shape transition on increasing confinement as shown by our investigation using molecular simulations. In channels this weak-to-strong confinement transition leads to extended conformations without the hairpin-like back-folding. In cavities, on decrease of cavity radius, the semi-flexible chain in a disordered state starts to self-organize into the torus. As a common rule for both types of confinement the transition to the ordered structures is observed when the radius of cavity and cylindrical channel reaches the lower bound of macromolecular flexibility given by the average typical radius of curvature of the chain, which is approximately equal to the persistence length of the macromolecular chain. This simple geometric rule finds its application in various confinement situations of stiff bio-macromolecules either in micro-channel experiments or in real biophysical situation, such as DNA in viral capsid.     

Crowding-induced structural alterations of random-loop chromosome model

We investigate structural alterations of random-loop polymers due to changes in the crowding condition, as a model to study environmental effects on the structure of chromosome subcompartments. The polymer structure is changed in a nonmonotonic fashion with an increasing density of crowders: condensed at small volume fractions; decondensed at high crowding volume fractions. The nonmonotonic behavior is a manifestation of the nontrivial distance dependence of the depletion interactions. We also show that crowding-induced structural alterations affect the access of binding proteins to the surface of polymer segments and are distinguished from structural changes due to the increased number of specific polymer loops.     

Demixing and nematic behaviour of oblate hard spherocylinders and hard spheres mixtures: Monte Carlo simulation and Parsons–Lee theory

Parsons–Lee approach is formulated for the isotropic–nematic transition in a binary mixture of oblate hard spherocylinders and hard spheres. Results for the phase coexistence and for the equation of state in both phases for fluids with different relative size and composition ranges are presented. The predicted behaviour is in agreement with Monte Carlo simulations in a qualitative fashion. The study serves to provide a rational view of how to control key aspects of the behaviour of these binary nematogenic colloidal systems. This behaviour can be tuned with an appropriate choice of the relative size and molar fractions of the depleting particles. In general, the mixture of discotic and spherical particles is stable against demixing up to very high packing fractions. We explore in detail the narrow geometrical range where demixing is predicted to be possible in the isotropic phase. The influence of molecular crowding effects on the stability of the mixture when spherical molecules are added to a system of discotic colloids is also studied.     

Phase transitions for an ideal Bose condensate trapped in?a?quartic potential

Based on the classification scheme of phase transitions, we study the phase transitions for an ideal Bose gas with a finite number of particles confined in a three-dimensional quartic trap. We show that the phase transition of an ideal Bose gas in the three-dimensional quartic trap is of third order for finite particle numbers, quite different from the fact that the phase transition is of first order in the thermodynamic limit. We discuss the effects of finite particle numbers on the nature of the phase transitions, and determine the dependence of transition temperature on particle number.     

Thermodynamics,phase transitions and Ruppeiner geometry for Einstein–dilaton–Lifshitz black holes in the presence of Maxwell and Born–Infeld electrodynamics

In this paper, we first obtain the higher-dimen-sional dilaton–Lifshitz black hole solutions in the presence of Born–Infeld (BI) electrodynamics. We find that there are two different solutions for the cases of \(z=n+1\) and \(z\ne n+1\) where z is the dynamical critical exponent and n is the number of spatial dimensions. Calculating the conserved and thermodynamical quantities, we show that the first law of thermodynamics is satisfied for both cases. Then we turn to the study of different phase transitions for our Lifshitz black holes. We start with the Hawking–Page phase transition and explore the effects of different parameters of our model on it for both linearly and BI charged cases. After that, we discuss the phase transitions inside the black holes. We present the improved Davies quantities and prove that the phase transition points shown by them are coincident with the Ruppeiner ones. We show that the zero temperature phase transitions are transitions in the radiance properties of black holes by using the Landau–Lifshitz theory of thermodynamic fluctuations. Next, we turn to the study of the Ruppeiner geometry (thermodynamic geometry) for our solutions. We investigate thermal stability, interaction type of possible black hole molecules and phase transitions of our solutions for linearly and BI charged cases separately. For the linearly charged case, we show that there are no phase transitions at finite temperature for the case \( z\ge 2\). For \(z<2\), it is found that the number of finite temperature phase transition points depends on the value of the black hole charge and there are not more than two. When we have two finite temperature phase transition points, there is no thermally stable black hole between these two points and we have discontinuous small/large black hole phase transitions. As expected, for small black holes, we observe finite magnitude for the Ruppeiner invariant, which shows the finite correlation between possible black hole molecules, while for large black holes, the correlation is very small. Finally, we study the Ruppeiner geometry and thermal stability of BI charged Lifshtiz black holes for different values of z. We observe that small black holes are thermally unstable in some situations. Also, the behavior of the correlation between possible black hole molecules for large black holes is the same as for the linearly charged case. In both the linearly and the BI charged cases, for some choices of the parameters, the black hole system behaves like a Van der Waals gas near the transition point.     

用单分子磁镊研究顺铂导致的DNA凝聚

本文报道了用单分子磁镊研究抗癌药顺铂导致的DNA凝聚过程.结果表明,当拉力比较小时,DNA凝聚的长度-时间曲线是连续缩短和阶跃缩短并存的复杂曲线.而当拉力较大但又不足以阻止DNA的凝聚时,凝聚曲线为连续缩短的双曲线.增加顺铂浓度只会增大凝聚速度而不会改变反应曲线的形状.实验结果与下列成环凝聚模型一致：在水溶液中顺铂能够与DNA形成双臂加合物,也能形成单臂加合物.当顺铂使DNA长链上相距较远的碱基间发生远程交联时,形成小环,导致DNA凝聚.小环间的进一步交联会引起DNA的完全凝聚.DNA凝聚产物十分稳定. 关键词： 顺铂 DNA凝聚 单分子操纵 抗癌药     

On the freezing and structure of hard spheres under spherical confinement

The equation of state and the structure of hard spheres confined in spherical pores have been investigated via molecular dynamics for different pore radii ranging from 5.0 to 10.0?σ, where σ is the particle diameter. The hard boundary is chosen to capture the pure geometric effect of spherical confinement. A discontinuity in the equation of state was observed, indicating the onset of a freezing-like phase transition, which was similar to that of the bulk hard-sphere fluids. The behaviour of confined particles resembles that of the bulk with increase in the pore size, while its deviation from the bulk is found to be larger at the solid-like phase. For the pore radius below 5.0, FCC-like crystal clusters are not formed in spherically confined hard spheres.     

Effective field study of the magnetism and superconductivity in idealised Ising-type X@Y60 endohedral fullerene system

In this study, effective-field calculations within Ising model framework have been utilised to investigate theoretically the effect of temperature and interaction parameters on the magnetic and hysteretic processes in an idealised system used to represent endohedral fullerene (EF) with a dopant magnetic atom confined within a spherical cage. The thermal behaviour of the partial (centre and surface) and the total magnetizations are studied to determine the character of phase transition (continuous and discontinuous) and to elaborate the phase diagram in interaction parameters plane. The total and partial hysteresis curves with susceptibility peaks and coercive fields are also given and focused on the influence of the temperature and interaction parameters. According to values of Hamiltonian parameters, the system exhibits the first- and second-order phase transitions and three types of compensation behaviour, namely Q-, R-, and S-types. In the phase diagram of the system, when the centre–surface (C–S) interaction increases or decreases, the phase transition temperature increases symmetrically. Finally, from the hysteresis curves of the system, we observed that type II superconducting-like behaviour can appear by the presence of dopant centre magnetic atom.     

Nucleation on a sphere: the roles of curvature,confinement and ensemble

ABSTRACT

By combining Monte Carlo simulations and analytical models, we demonstrate and explain how the gas-to-liquid phase transition of colloidal systems confined to a spherical surface depends on the curvature and size of the surface, and on the choice of thermodynamic ensemble. We find that the geometry of the surface affects the shape of the free energy profile and the size of the critical nucleus by altering the perimeter–area ratio of isotropic clusters. Confinement to a smaller spherical surface results in both a lower nucleation barrier and a smaller critical nucleus size. Furthermore, the liquid domain does not grow indefinitely on a sphere. Saturation of the liquid density in the grand canonical ensemble and the depletion of the gas phase in the canonical ensemble lead to a minimum in the free energy profile, with a sharp increase in free energy for additional growth beyond this minimum.     

Quantum corrections to the thermodynamics and phase transition of a black hole surrounded by a cavity in the extended phase space

In the extended phase space, we investigate the rainbow gravity-corrected thermodynamic phenomena and phase structure of the Schwarzschild black hole surrounded by a spherical cavity. The results show that rainbow gravity has a very significant effect on the thermodynamic phenomena and phase structure of the black hole. It prevents the black hole from total evaporation and leads to a remnant with a limited temperature but no mass. Additionally, we restore the P − V criticality and obtain the critical quantities of the canonical ensemble. When the temperature or pressure is smaller than the critical quantities, the system undergoes two Hawking-Page-like phase transitions and one first-order phase transition, which never occurs in the original case. Remarkably, our findings demonstrate that the thermodynamic behavior and phase transition of the rainbow SC black hole surrounded by a cavity in the extended phase space are analogous to those of the Reissner–Nordström anti-de Sitter black hole. Therefore, rainbow gravity activates the effect of electric charge and cutoff factor in the evolution of the black hole.     

Selectivity and temperature dependence of phase and phase transition in diblock copolymer solution

In order to study the effects of solvent selectivity and temperature on phase behavior and transition of diblock copolymer solution, self-consistent field theory is modified to incorporate the short-range interaction and non-local effects. Inhomogeneous free-energy density is shown to be dependent on solvent selectivity, temperature and copolymer concentration. Enthalpic quantity and entropic contributions are crucial to phase diagrams of diblock copolymer solution. Three selective strengths of solvent --weak, moderate and strong-- are chosen for comparison. For a weakly selective solvent, theoretical and experimental results illustrate the same variation tendency in the phase boundary of the order-disorder transition for a symmetric diblock of polystyrene and polyisoprene. Self-consistent field equations can be used to calculate the exact FCC-BCC structural phase transition temperatures in moderately and strongly selective solvents. Detailed comparison with the experimental phase diagrams including lamellar, cylindrical and spherical structures is presented.     

Effect of Interaction upon Translocation of Confined Polymer Chain Through Nanopore

运用二维的键长涨落模型和蒙特卡洛方法研究高分子链从一个受限空间到自由空间穿孔过程中,链单体与纳米孔之间的相互作用.结果表明,在不同的链长和纳米孔交互作用下,高分子链成功穿越自由能能垒取决于链长和纳米孔长度,并且由于交互作用降低了自由能能垒,导致高分子链在纳米管的平均捕获时间缩短.     

在NaCl和HTAB共存条件下甲基纤维素溶液凝胶化行为

利用流变仪研究了甲基纤维素(MC)溶液在NaCl、十六烷基三甲基溴化铵(HTAB)以及两者共存下MC溶液的凝胶化行为,发现其凝胶化温度随着NaCl浓度的增加而下降,随着HTAB浓度的增加而上升;但是MC/NaCl的凝胶化温度保持不变,与HTAB浓度 无关,而MC/HTAB溶液的凝胶化温度则随着NaCl浓度的增加而下降．以上的实验结果表明,在NaCl存在下,HTAB将被诱导形成胶束,因此MC/NaCl的凝胶化温度保持不变;反之,当NaCl不存在时,HTAB将优先吸附到MC上而不会在溶液中形成胶束,尽管其浓度     

Inter-lamellar interactions modulated by addition of guest components

We have investigated the effects of a guest component (polymer or spherical colloidal particle) confined between flexible lamellar slits on the inter-lamellar interaction by means of a small-angle X-ray scattering technique and a neutron spin echo technique. The dominant interaction between flexible lamellar membranes without guest components is the Helfrich mechanism. The addition of a neutral polymer into the lamellar phase induces an attractive inter-lamellar interaction and finally destabilizes the lamellar phase. On the other hand, spherical colloidal particles confined between flexible lamellar membranes reduce the undulational fluctuations of lamellae and bring a repulsive inter-lamellar interaction. The behavior of the layer compression modulus of the lamellar membrane containing colloidal particles is well described by the entropical repulsive inter-lamellar interaction driven by steric hindrance.Received: 26 March 2004, Published online: 4 May 2004PACS: 82.70.Uv Surfactants, micellar solutions, vesicles, lamellae, amphiphilic systems, (hydrophilic and hydrophobic interactions) - 61.25.Hq Macromolecular and polymer solutions; polymer melts; swelling - 83.80.Hj Suspensions, dispersions, pastes, slurries, colloids - 89.75.Fb Structures and organization in complex systems     

Dyson equation for transverse ising paramagnet

The behavior of a confined magnetized ideal boson gas is examined. The effects of the dimensionalities of the system and the confinement potential as well as the effects of the field strength on the Bose-Einstein condensation are analyzed. It is shown that a phase transition does not occur in strongly confined systems. For the weakly confined gas a connection with the results of the non-confined magnetized gas is made. A correspondence is established between our results and those of a free gas of different dimensionality. The density of states of a particle moving in a three-dimensional space and confined by a cylindrically symmetric potential is calculated and used to explain the correspondence. The thermodynamic properties of the 3D - 2d gas are worked out in detail.     

液晶胆甾相中的分子短程关联

向列相液晶的二粒子集团理论被推广应用于研究胆甾相二维模型.手征性分子固定在三维简单立方晶格的格点上,而分子取向限制在二维.理论结果表明,平衡态螺旋波矢依赖于温度的变化,且存在胆甾相到向列相相变.通过考虑分子间短程关联,二粒子集团理论的数值结果较平均场理论更接近Monte Carlo模拟结果.     

BCS-BEC crossover in mix-dimensional Fermi gases

We investigate a mix-dimensional Fermi-Fermi mixtures in which one species is confined in two-dimensional (2D) space while the other is free in three-dimensional space (3D). We determine the superfluid transition temperature T _c for the entire BCS-BEC crossover including the important effects of noncondensed pairs. We find that the transition temperature reduces while the imbalance of mass is increased or lattice spacing is reduced. In spin imbalance case, the stability of superfluid is sharply destroyed by increasing the polarization.     

Effect of Spherical Nanoparticles on the Motion of Macromolecular Chains and Segments of Isotactic Polypropylene. I. Dynamic Mechanical and Thermal Properties

The role of spherical nano-CaCO₃ particles treated with 2 wt% and 6 wt% stearic acid (SA), respectively, on the motion of macromolecular chains and segments of isotactic polypropylene (iPP) was studied through the dynamic mechanical analysis and nonisothermal crystallization. Higher nucleation activity of the particles and more nucleating sites were achieved in the 6 wt% SA treated particle nanocomposites with respect to the 2 wt% SA counterpart. The increased nucleation efficiency caused high inhomogeneity and thus large mobility of the amorphous phase of iPP, which favored a low glass transition temperature (T_g ) in the nanocomposites. However, the spherical nanoparicles also spatially restrained the motion of macromolecular chains and segments, and the better the nanoparticles dispersed, the stronger the restriction was. Thus the glass transition temperature (T_g ) of the nanocomposites decreased with increasing filler loading but recovered at a certain particle concentration. At this filler content, the maximal α-transition temperature (T_α ) and the main melting peak temperature (T_m1 ) as well as the lowest degree of crystallinity (X_PP ) also occurred. This critical filler loading appeared at lower value (20 wt%) in 6 wt% SA treated nano-CaCO₃ composites with respect to 2 wt% SA counterpart (25%) due to the better dispersion of particles in the former. It was concluded that the mobility of the macromolecular chains and segments of iPP was dominated by the competition of the spatial confinement and nucleation effect of nano-CaCO₃ particles in the matrix.