Dissipative particle dynamics simulation study of the bilayer-vesicle transition

A bilayer structure is an important immediate for the vesicle formation. However,the mechanism for the bilayer-vesicle transition remains unclear. In this work,a dissipative particle dynamics(DPD) simulation method was employed to study the mechanism of the bilayer-vesicle transition. A coarse-grained model was built based on a lipid molecule termed dimyristoylphosphatidylcholine(DMPC). Simulations were performed from two different initial configurations:a random dispersed solution and a tensionless bilayer. It was found that the bilayer-vesicle transition was driven by the minimization of the water-tail hydrophobic interaction energy,and was accompanied with the increase of the position entropy due to the redistribution of water molecules. The bulk pressure was reduced during the bilayer-vesicle transition,suggesting the evolved vesicle morphology was at the relatively low free energy state. The membrane in the product vesicle was a two-dimensional fluid. It can be concluded that the membrane of a vesicle is not interdigitated and most of the bonds in lipid chains are inclined to orient along the radical axis of the vesicle.     

Structural transitions at solid-liquid interfaces

In this paper we present the findings of our investigations using molecular dynamics, on molecularly thin films of n-octane confined between topographically smooth solid surfaces. We focus on the effect of increasing solid surface-methylene unit energetic affinity and the effect of increasing pressure (normal load) of the film in inducing liquid-solid phase transitions. We observed an abrupt transition in the structural features of the film at a critical value of the characteristic energy that quantified the affinity between solid surfaces and methylene units. This energetically driven transition was evident from the discontinuous increase of intermolecular order, a precipitous extension of the octane molecules and freezing of molecular migration and rotation. Increasing pressure had a similar effect in inducing a liquid-solid phase transition. The characteristics of the transition showed that it is a mild first order transition from a highly ordered liquid to a poorly organized solid. These findings demonstrate that the solidification of nanoscopically thin films of linear alkanes is a general phenomenon (driven either energetically or by increasing pressure), and does not require the aid of commensurate surface topography.     

Generation of initial trajectories for transition path sampling of chemical reactions with ab initio molecular dynamics

Transition path sampling is an innovative method for focusing a molecular dynamics simulation on a reactive event. Although transition path sampling methods can generate an ensemble of reactive trajectories, an initial reactive trajectory must be generated by some other means. In this paper, the authors have evaluated three methods for generating initial reactive trajectories for transition path sampling with ab initio molecular dynamics. The authors have tested each of these methods on a set of chemical reactions involving the breaking and making of covalent bonds: the 1,2-hydrogen elimination in the borane-ammonia adduct, a tautomerization, and the Claisen rearrangement. The first method is to initiate trajectories from the potential energy transition state, which was effective for all reactions in the test set. Assigning atomic velocities found using normal mode analysis greatly improved the success of this method. The second method uses a high temperature molecular dynamics simulation and then iteratively reduces the total energy of the simulation until a low temperature reactive trajectory is found. This was effective in generating a low temperature trajectory from an initial trajectory run at 3000 K of the tautomerization reaction, although it failed for the other two. The third uses an orbital based bias potential to find a reactive trajectory and uses this trajectory to initiate an unbiased trajectory. The authors found that a highest occupied molecular orbital-lowest unoccupied molecular orbital bias could be used to find a reactive trajectory for the Claisen rearrangement, although it failed for the other two reactions. These techniques will help make it practical to use transition path sampling to study chemical reaction mechanisms that involve bond breaking and forming.     

Randomized tree construction algorithm to explore energy landscapes

In this work, a new method for exploring conformational energy landscapes is described. The method, called transition-rapidly exploring random tree (T-RRT), combines ideas from statistical physics and robot path planning algorithms. A search tree is constructed on the conformational space starting from a given state. The tree expansion is driven by a double strategy: on the one hand, it is naturally biased toward yet unexplored regions of the space; on the other, a Monte Carlo-like transition test guides the expansion toward energetically favorable regions. The balance between these two strategies is automatically achieved due to a self-tuning mechanism. The method is able to efficiently find both energy minima and transition paths between them. As a proof of concept, the method is applied to two academic benchmarks and the alanine dipeptide.     

Hydration of dimethyldodecylamine-N-oxide: enthalpy and entropy driven processes

Dimethyldodecylamine-N-oxide (DDAO) has only one polar atom that is able to interact with water. Still, this surfactant shows very hydrophilic properties: in mixtures with water, it forms normal liquid crystalline phases and micelles. Moreover, there is data in the literature indicating that the hydration of this surfactant is driven by enthalpy while other studies show that hydration of surfactants and lipids typically is driven by entropy. Sorption calorimetry allows resolving enthalpic and entropic contributions to the free energy of hydration at constant temperature and thus directly determines the driving forces of hydration. The results of the present sorption calorimetric study show that the hydration of liquid crystalline phases of DDAO is driven by entropy, except for the hydration of the liquid crystalline lamellar phase which is co-driven by enthalpy. The exothermic heat effect of the hydration of the lamellar phase arises from formation of strong hydrogen bonds between DDAO and water. Another issue is the driving forces of the phase transitions caused by the hydration. The sorption calorimetric results show that the transitions from the lamellar to cubic and from the cubic to the hexagonal phase are driven by enthalpy. Transitions from solid phases to the liquid crystalline lamellar phase are entropically driven, while the formation of the monohydrate from the dry surfactant is driven by enthalpy. The driving forces of the transition from the hexagonal phase to the isotropic solution are close to zero. These sorption calorimetric results are in good agreement with the analysis of the binary phase diagram based on the van der Waals differential equation. The phase diagram of the DDAO-water system determined using DSC and sorption calorimetry is presented.     

Dynamical origin of enhanced conformational searches of Tsallis statistics sampling

The characteristic sampling dynamics of importance samplings driven by the Tsallis weight [C. Tsallis, J. Stat. Phys. 52, 479 (1988)] has been analyzed in terms of recently developed Langevin stochastic model by considering the effects of the density of states and the potential smoothing of the Tsallis transformation. Our study reveals that the fixed points, which are determined by the crossing points of the statistical temperature and the Tsallis effective temperature, play a critical role in overall dynamics of the Tsallis statistics sampling. The dynamical origin of enhanced conformational searches of the Tsallis weight has been investigated by unveiling the intimate relationship between the sampling dynamics and the stability change of corresponding fixed points. Based on this stochastic analysis, we propose one effective method to realize a broad energy distribution in the Tsallis statistics sampling by determining optimal Tsallis parameters systematically based on preliminary canonical samplings. The effectiveness of our method has been validated in the folding simulation of Met-Enkephalin and liquid-solid transition simulation of Lennard-Jones cluster systems.     

Structural and dynamical properties of transition metal clusters

Results of molecular dynamics simulation studies of structural and dynamical properties of 12-, 13-, and 14-atom transition metal clusters are presented. The calculations are carried out using a Gupta-like potential expressed in reduced units. The transformation to absolute units involves two size-dependent parameters which effectively convert the potential into a size-dependent one. The minimum energy geometries of the clusters are obtained through the technique of simulated thermal quenching. A melting-like transition is observed as the energy of the clusters is increased. A novel element of the transition is that it may involve a premelting state.     

Molecular Dynamics Simulation Studies on the Cooling Process of Polyvinyl Chloride

IntroductionRecently,molecular dynamics(MD)simulationhas been used extensively in the study of polymer sys-tems[1—11].The increased interest in computer simula-tion is assisted by the fast evolution of computer tech-nology,which makes molecular simulatio…     

Efficient combination of Wang-Landau and transition matrix Monte Carlo methods for protein simulations

An efficient combination of the Wang-Landau and transition matrix Monte Carlo methods for protein and peptide simulations is described. At the initial stage of simulation the algorithm behaves like the Wang-Landau algorithm, allowing to sample the entire interval of energies, and at the later stages, it behaves like transition matrix Monte Carlo method and has significantly lower statistical errors. This combination allows to achieve fast convergence to the correct values of density of states. We propose that the violation of TTT identities may serve as a qualitative criterion to check the convergence of density of states. The simulation process can be parallelized by cutting the entire interval of simulation into subintervals. The violation of ergodicity in this case is discussed. We test the algorithm on a set of peptides of different lengths and observe good statistical convergent properties for the density of states. We believe that the method is of general nature and can be used for simulations of other systems with either discrete or continuous energy spectrum.     

分子模拟在有机聚合物电致发光材料设计中的应用

对聚合物分子模拟理论和一种较为精确的聚合物模拟方法－地简要的介绍，分析模拟计算的结果如能量结构、前线轨道能级、能带结构、跃迁能等与电致发光相关的测定指标如导电性、氧化还原电位、光电子能谱、吸收与发光谱、光氧化性、热稳定性相关联。并讨论了分子模拟辅助电致发光新材料设计上的应用。     

水电解制氢非贵金属催化剂的研究进展

氢能作为零碳排放能源是被公认的最清洁能源之一,如何有效可持续地产氢是未来人类步入氢能经济首先要解决的问题。电解水技术基于电化学分解水的原理,利用可再生电能或太阳能驱动水分解为氢气和氧气,被认为是最有前途和可持续性的产氢途径。然而,无论是光解水还是电解水,均需要高活性、高稳定性的非贵金属氢析出和氧析出催化剂以使水电解反应经济节能。本文介绍了我们研究所近三年在水电解方面的研究进展,其中着重介绍了：（ⅰ）氢析出催化剂,包括利用低温磷化过渡金属（氢）氧化物的方法制备过渡金属磷化物,同时过渡金属硫化物、硒化物以及碳化物等均被成功合成并被应用为有效的阴极析氢催化剂;（ⅱ）氧析出催化剂,主要包括金属磷化物、硫化物、氧化物/氢氧化物等;（ⅲ）双功能催化剂,主要包括过渡金属磷化物、硒化物、硫化物等。最后,总结展望了发展水电解非贵金属催化剂所面临的挑战与未来发展方向。     

Prospects of transition interface sampling simulations for the theoretical study of zeolite synthesis

The transition interface sampling (TIS) technique allows large free energy barriers to be overcome within reasonable simulation time, which is impossible for straightforward molecular dynamics. Still, the method does not impose an artificial driving force, but it surmounts the timescale problem by an importance sampling of true dynamical pathways. Recently, it was shown that the efficiency of TIS when calculating reaction rates is less sensitive to the choice of reaction coordinate than those of the standard free energy based techniques. This could be an important advantage in complex systems for which a good reaction coordinate is usually very difficult to find. We explain the principles of this method and discuss some of the promising applications related to zeolite formation.     

A transition path sampling study of the reaction catalyzed by the enzyme chorismate mutase

The study of the chemical steps in enzyme-catalyzed reactions represents a challenge for molecular simulation techniques. One concern is how to calculate paths for the reaction. Common techniques include the definition of a reaction coordinate in terms of a small set of (normally) geometrical variables or the determination of minimum energy paths on the potential energy surface of the reacting system. Both have disadvantages, the former because it presupposes knowledge of which variables are likely to be important for reaction and the latter because it provides a static picture and dynamical effects are ignored. In this paper, we employ the transition path sampling method developed by Chandler and co-workers, which overcomes some of these limitations. The reaction that we have chosen is the chorismate-mutase-catalyzed conversion of chorismate into prephenate, which has become something of a test case for simulation studies of enzyme mechanisms. We generated an ensemble of approximately 1000 independent transition paths for the reaction in the enzyme and another approximately 500 for the corresponding reaction in solution. A large variety of analyses of these paths was performed, but we have concentrated on characterizing the transition state ensemble, particularly the flexibility of its structures with respect to other ligands of the enzyme and the time evolution of various geometrical and energetic properties as the reaction proceeds. We have also devised an approximate technique for locating transition state structures along the paths.     

Probability distributions of molecular observables computed from Markov models

Molecular dynamics (MD) simulations can be used to estimate transition rates between conformational substates of the simulated molecule. Such an estimation is associated with statistical uncertainty, which depends on the number of observed transitions. In turn, it induces uncertainties in any property computed from the simulation, such as free energy differences or the time scales involved in the system's kinetics. Assessing these uncertainties is essential for testing the reliability of a given observation and also to plan further simulations in such a way that the most serious uncertainties will be reduced with minimal effort. Here, a rigorous statistical method is proposed to approximate the complete statistical distribution of any observable of an MD simulation provided that one can identify conformational substates such that the transition process between them may be modeled with a memoryless jump process, i.e., Markov or Master equation dynamics. The method is based on sampling the statistical distribution of Markov transition matrices that is induced by the observed transition events. It allows physically meaningful constraints to be included, such as sampling only matrices that fulfill detailed balance, or matrices that produce a predefined equilibrium distribution of states. The method is illustrated on mus MD simulations of a hexapeptide for which the distributions and uncertainties of the free energy differences between conformations, the transition matrix elements, and the transition matrix eigenvalues are estimated. It is found that both constraints, detailed balance and predefined equilibrium distribution, can significantly reduce the uncertainty of some observables.     

Preorganization and reorganization as related factors in enzyme catalysis: the chorismate mutase case

In this paper a deeper insight into the chorismate-to prephenate-rearrangement, catalyzed by Bacillus subtilis chorismate mutase, is provided by means of a combination of statistical quantum mechanics/molecular mechanics simulation methods and hybrid potential energy surface exploration techniques. The main aim of this work is to present an estimation of the preorganization and reorganization terms of the enzyme catalytic rate enhancement. To analyze the first of these, we have studied different conformational equilibria of chorismate in aqueous solution and in the enzyme active site. Our conclusion is that chorismate mutase preferentially binds the reactive conformer of the substrate--that presenting a structure similar to the transition state of the reaction to be catalyzed--with shorter distances between the carbon atoms to be bonded and more diaxial character. With respect to the reorganization effect, an energy decomposition analysis of the potential energies of the reactive reactant and of the reaction transition state in aqueous solution and in the enzyme shows that the enzyme structure is better adapted to the transition structure. This means not only a more negative electrostatic interaction energy with the transition state but also a low enzyme deformation contribution to the energy barrier. Our calculations reveal that the structure of the enzyme is responsible for stabilizing the transition state structure of the reaction, with concomitant selection of the reactive form of the reactants. This is, the same enzymatic pattern that stabilizes the transition structure also promotes those reactant structures closer to the transition structure (i.e., the reactive reactants). In fact, both reorganization and preorganization effects have to be considered as the two faces of the same coin, having a common origin in the effect of the enzyme structure on the energy surface of the substrate.     

Heating matter with heavy ion beams

Heating dense matter with intense beams from heavy ion accelerators to temperatures of 1–1000 eV is explored in terms of models and numerical simulation. The emphasis is on the target configuration, the region of plasma parameters that can be reached, on heavy ion energy deposition in hot dense matter, and on the hydrodynamic and radiative target response. Accelerator options for this purpose and their scaling with ion energy are discussed. Inertial confinement fusion driven by heavy ion beams is one of the major motivations for this research, and the present paper provides practical tools for future experiments in this direction.     

A hybrid potential reaction path and free energy study of the chorismate mutase reaction.

We present a combination of two techniques--QM/MM statistical simulation methods and QM/MM internal energy minimizations--to get a deeper insight into the reaction catalyzed by the enzyme chorismate mutase. Structures, internal energies and free energies, taken from the paths of the reaction in solution and in the enzyme have been analyzed in order to estimate the relative importance of the reorganization and preorganization effects. The results we obtain for this reaction are in good agreement with experiment and show that chorismate mutase achieves its catalytic efficiency in two ways; first, it preferentially binds the active conformer of the substrate and, second, it reduces the free energy of activation for the reaction relative to that in solution by providing an environment which stabilizes the transition state.     

Theoretical analysis on changes in thermodynamic quantities upon protein folding: essential role of hydration

The free energy change associated with the coil-to-native structural transition of protein G in aqueous solution is calculated by using the molecular theory of solvation, also known as the three-dimensional reference interaction site model theory, to uncover the molecular mechanism of protein folding. The free energy is decomposed into the protein intramolecular energy, the hydration energy, and the hydration entropy. The folding is accompanied with a large gain in the protein intramolecular energy. However, it is almost canceled by the correspondingly large loss in the hydration energy due to the dehydration, resulting in the total energy gain about an order of magnitude smaller than might occur in vacuum. The hydration entropy gain is found to be a substantial driving force in protein folding. It is comparable with or even larger than the total energy gain. The total energy gain coupled with the hydration entropy gain is capable of suppressing the conformational entropy loss in the folding. Based on careful analysis of the theoretical results, the authors present a challenging physical picture of protein folding where the overall folding process is driven by the water entropy effect.     

Effects of melting and ordering on the isosteric heat and monolayer density of argon adsorption on graphite

The aim of this paper is to study the effects of temperature on the state of the adsorbed argon on an uniform graphite surface. We applied the kinetic Monte Carlo scheme to simulate adsorption over a very wide range of temperature, which allows us to model the vapor–solid, the vapor–liquid and the order–disorder transition of the monolayer. The main distinction of our methodology is that it accounts for the lattice constant change with loading in the case of formation of an ordered molecular layer by appropriately changing the simulation box size. To do this we enforced the equality of the tangential pressures obtained by the virial and thermodynamic routes, which corresponds to the minimum Helmholtz free energy of a system at a given number of molecules and volume. This criterion is a consequence of the Gibbs–Duhem equation. A significant result obtained by application of the new simulation method was a sharp contraction of the monolayer just after its completion and the onset of the second layer. It manifests itself in an additional heat release. We re-determined the 2D-melting and 2D-critical temperatures of the molecular layer of argon. We also analyzed the order–disorder transition above the 2D-melting and showed that it could occur at some temperatures above the 2D-critical temperature. In this case, a hexagonal lattice appears at a sufficiently large tangential pressure. The effects of loading on the lattice constant, the 2D-critical temperature of the order–disorder transition and the differential heat of adsorption are thoroughly discussed.