DNA conformation in nanochannels: Monte Carlo simulation studies using a primitive DNA model

We have performed canonical ensemble Monte Carlo simulations of a primitive DNA model to study the conformation of 2.56 ~ 21.8 μm long DNA molecules confined in nanochannels at various ionic concentrations with the comparison of our previous experimental findings. In the model, the DNA molecule is represented as a chain of charged hard spheres connected by fixed bond length and the nanochannels as planar hard walls. System potentials consist of explicit electrostatic potential along with short-ranged hard-sphere and angle potentials. Our primitive model system provides valuable insight into the DNA conformation, which cannot be easily obtained from experiments or theories. First, the visualization and statistical analysis of DNA molecules in various channel dimensions and ionic strengths verified the formation of locally coiled structures such as backfolding or hairpin and their significance even in highly stretched states. Although the folding events mostly occur within the region of ~0.5 μm from both chain ends, significant portion of the events still take place in the middle region. Second, our study also showed that two controlling factors such as channel dimension and ionic strength widely used in stretching DNA molecules have different influence on the local DNA structure. Ionic strength changes local correlation between neighboring monomers by controlling the strength of electrostatic interaction (and thus the persistence length of DNA), which leads to more coiled local conformation. On the other hand, channel dimension controls the overall stretch by applying the geometric constraint to the non-local DNA conformation instead of directly affecting local correlation. Third, the molecular weight dependence of DNA stretch was observed especially in low stretch regime, which is mainly due to the fact that low stretch modes observed in short DNA molecules are not readily accessible to much longer DNA molecules, resulting in the increase in the stretch of longer DNA molecules.     

Monte Carlo studies of tethered chains

Monte Carlo computer simulations of end-tethered chains grafted onto a hard wall have been performed. The chains were modeled as self-avoiding chains on a cubic lattice at athermal solvent conditions. The simulations spanned a wide range of chain lengths, N (100–1000, i.e., up to molecular weights of a few hundred thousands), and anchoring densities, σ (2 × 10⁻⁴ to 0.4), to properly chart the relevant parameter space. It is shown that the reduced surface coverage σ* = σπR is the most appropriate variable that quantitatively determines the mushroom, overlapping mushroom and brush regimes, where R_g is the radius of gyration of a free chain in solution. The simulation data are analyzed to determine the conformational characteristics and shape of the anchored chains and to compare them with the predictions of the analytical self consistent field theory. The strong stretching limit of the theoretical predictions is obtained only for σ* > 8. © 2009 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 47:2449–2461, 2009     

Dynamic Monte Carlo Simulation of ATRP in a Batch Reactor

A dynamic MC model was developed to simulate the polymerization kinetics and the detailed microstructure of copolymers made with ATRP in a batch reactor. The model was used to predict monomer conversion, average molecular weight, polydispersity index, and copolymer composition as a function of polymerization time. The model can also predict the distribution of molecular weight, chemical composition, and comonomer sequence length at any polymerization time or comonomer conversion. The simulation was used to explore the effects of rate constants and reactant stoichiometry on the microstructure of chains. Two copolymerization systems were chosen to demonstrate the effect of reactivity ratios and comonomer feed compositions on the final chemical composition distribution.

     

蒙特卡洛模拟在分子模拟教学中的应用*

以有机化合物的模板诱导沉积实验为例,介绍了蒙特卡洛模拟在分子模拟教学中的应用。本实验在有机化合物诱导沉积实验的基础上,将诱导沉积实验、蒙特卡洛模拟方法系统综合在一个实验教学中,让学生在学习蒙特卡洛模拟方法的同时,更直观、形象地理解分子间相互作用对有机分子聚集形貌的影响,加深学生对有机分子自组装概念的理解。通过实际上机操作,学生还能初步了解Dev-C++,RasMol等相关软件的使用,并加深学生对结构化学及计算化学课程相关知识的理解。     

自由基聚合反应的Monte Carlo模拟方法

本文将化学反应动力学的MonteCarlo模拟方法运用到引发剂引发的自由基聚合反应的非稳态动力学,针对自由基聚合反应动力学数值模拟所特有的"无伸缩问题",采用"偏倚抽样法"解决了MonteCarlo模拟中的"无伸缩问题",模拟结果与非稳态动力学解的结果完全一致,此算法易推广到研究更复杂的自由基聚合反应体系。     

Simulation of polymers by the Monte Carlo method using the Wang-Landau algorithm

Studies of several models of polymers with the use of a version of the Monte Carlo method—entropy sampling combined with the Wang-Landau algorithm—are presented. This approach allows derivation of the energy distribution function over a broad energy range. On the basis of this distribution various thermal characteristics of the systems are calculated in a wide temperature range: internal energy, free energy, heat capacity, average gyration radius, and mean end-to-end distance. For simple continuum and lattice models of free chains and rings we consider the athermal case, with eliminated overlaps, and the thermal case, when nonvalence interactions between units at finite distances are accounted for. In the framework of the proposed approaches, the models of alkanes and the simplest polypeptide, polyglycine, and the lattice model of flexible polyelectrolyte are investigated.     

Monte Carlo simulation studies of polymer systems

Polymers molecules in solution or melt are more or less flexible and continuously change their shape and size. Thus, characteristic properties of the system fluctuate around statistical mean values which are dependent on the concentration of the solution, on the quality of the solvent used, and on the specific structure of the molecules, e.g. linear or star-branched. The most direct approach to these quantities on a molecular level are computer simulations. Due to restrictions of computer power fully atomistic simulations of macromolecules are presently still at the beginning but several arguments justify the use of simplified models. The most efficient way dealing with polymer systems are Monte Carlo simulations based on lattice chains, at least as long as static properties are of interest only. In the present paper a short introduction to the field is given and selected examples are presented in order to demonstrate the usefulness of these methods.     

Two-dimensional Monte Carlo studies of lipid molecules in a bilayer membrane

We present a new model to study in-plane liquid properties of lipid membranes. The different conformations of lipids are represented by a seven-state system of hard triatomic particles, or triples, of varying lengths which correspond to the different cross-sectional areas of the lipids in the plane of the membrane. Two-dimensional Monte Carlo simulations are performed in both the constant NVT and NPT ensembles. The distribution of states has a strong density dependence and a small temperature dependence over the biologically relevant range. There is no long range orientational order in the systems before freezing. The short range orientational order increases with density. Widom's particle insertion method is used to obtain the excess chemical potential of the system for the seven states. These values, along with the pressure, are in excellent agreement with estimates from scaled particle theory.     

Monte Carlo studies of a novel X-ray tube anode design

When energetic electrons are incident on high atomic number absorbers, a substantial fraction is back-scattered. This phenomenon is responsible for several undesirable effects in X-ray tubes, in particular a reduction in the X-ray output. The extent of this shortfall has been estimated by using Monte Carlo simulation to start electrons at increasing depth inside the anode, the results indicating that an output enhancement of nearly 50% could be achieved in principle if the electrons wasted in back-scatter events could be trapped inside a tungsten anode. To test this idea a further set of simulations were done for a novel anode geometry. Results showed that X-ray tube efficiencies might be substantially enhanced by this approach.     

Monte Carlo simulation of phase separation kinetics in a concentrated polymer solution

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表面活性剂与高分子链混合体系的模拟

计算机模拟了高分子链对表面活性剂胶束形成过程的影响，以及高分子链构象性质随胶束化过程的变化.结果表明,当高分子链与表面活性剂之间的相互作用强度超过临界值后，高分子链的存在有利于表面活性剂胶束的形成.临界聚集浓度（CAC）与临界胶束浓度（CMC）的比值CAC/CMC随高分子链长的增大和相互吸引作用的增强而减小.在CAC之前，高分子链与表面活性剂分子只有动态的聚集；但在CAC之后，表面活性剂胶束随表面活性剂浓度X的增加而增大，并静态地吸附在高分子链上，形成表面活性剂/高分子聚集体.随着表面活性剂分子的加入，高分子链的均方末端距和平均非球形因子先保持恒定；从X略小于CAC开始， 和快速减小，至极小值后又逐渐增大.模拟结果支持高分子链包裹在胶束表面的实验模型.     

三维格点中SAT链的Monte Carlo模拟

用MonteCarlo方法模拟了三维简立方格点和面心立方格点上的线性高分子模型自踪迹规避(Self AvoidingTrail,SAT ) .求解了SAT的各种临界指数 .所得的结果显示 ,SAT的各种临界指数介于无规行走 (RW )和自避行走 (SAW )之间 .这完全是因为体排斥作用对SAT模型的限制比对SAW的限制要少一些 ,但又比对RW的限制要大一些 .SAT的各种性质介于SAW和RW之间 .因此 ,有可能SAT与SAW不属于同一个普适类     

Quantum Monte Carlo study of first-row atoms using transcorrelated variational Monte Carlo trial functions

The effect of using the transcorrelated variational Monte Carlo (TC-VMC) approach to construct a trial function for fixed node diffusion Monte Carlo (DMC) energy calculations has been investigated for the first-row atoms, Li to Ne. The computed energies are compared with fixed node DMC energies obtained using trial functions constructed from Hartree-Fock and density functional levels of theory. Despite major VMC energy improvement with TC-VMC trial functions, no improvement in DMC energy was observed using these trial functions for the first-row atoms studied. The implications of these results on the nodes of the trial wave functions are discussed.     

Monte Carlo phase diagram for diblock copolymer melts

A partial phase diagram is constructed for diblock copolymer melts using lattice-based Monte Carlo simulations. This is done by locating the order-disorder transition (ODT) with the aid of a recently proposed order parameter and identifying the ordered phase over a wide range of copolymer compositions (0.2相似文献   

Monte Carlo Simulation of Thin Film Polymer Melts

We present Monte Carlo simulation data on conformations and dynamics of polymer melts confined in narrow slits of different widths and compare with data of bulk systems. We find that in confined geometries the chains swell laterally; they retain and even expand their spatially long-range correlations compared to bulk polymers and in contrast to the assumption of a complete screening of excluded volume. Long chains in bulk melts show entangled dynamics with a clear signature of a t^1/4-power law for the mean square displacements of innermost monomers at intermediate time scales. This behavior is gradually lost by confining the melts in slits with decreasing width. For ultra-thin films, the dynamics appears to follow a Rouse-like behavior over the entire subdiffusive regime. However, the terminal relaxation time is significantly increased compared to Rouse relaxation. This interesting observation was not reported previously and is the focus of our ongoing research.     

N2O分解反应的蒙特卡罗模拟

N2O作为大气污染物之一早已受到人们的注意，许多人研究了N2O在金属氧化物上的分解反应得到了一些基本的实验事实[1]：（1）反应速率与原料气中N2O的分压近似成比例．(2)在反应初期，N2的生成速率由大变小，O2的生成速率由小变大，达到平衡时，N2生成速率是O2生成速率的二倍．(3)过渡应答法研究表明，把原料气由N2O和He的混合气体切换成纯He后，N2立即停止发生，而O2的生成仍能维持一段时间．基于上述实验事实，人们对Nzo的催化分解反应提出了一些可能的机理，主要有下面两种看法：另一方面，人们还发现几O的催化分解反应是一个振荡…     

Monte Carlo Simulation of Polymer Reactions at Interfaces

Adhesion of immiscible polymers during two‐component injection moulding may be improved by transreactions of properly functionalised components. We performed MC simulations based on the three‐dimensional coarse‐grained bond fluctuation model (BFM) including a thermal interaction potential in with energy to characterise the behaviour of several selected types of chemical reactions, which are governed by activation energies of E_A = 0, 1, 3 and 5 k_BT. The consumption of reactive monomers for all the reactions in the time interval below the Rouse time τ_R exhibits a typical crossover from a kinetic‐controlled to a diffusion‐controlled behaviour and can be described by a bimolecular kinetic ansatz.

     

Complexation between a macromolecule and an amphiphile by Monte Carlo technique

Using a simple modified version of Larson's model, we studied the complexation between a macromolecule and an amphiphile in a dilute range of concentrations. The main characteristic of amphiphile molecules, that is, the hydrophobicity of the tails and hydrophilicity of the heads, is used to model the self-assembling process. Contrary to the molecular thermodynamics approaches, no prior shape was considered for the aggregates and the system was allowed to choose the most stable structure. For true ensemble averaging, without any synthetic results, configurational bias Monte Carlo and reptation moves are used to produce a Markov chain of configurations. From the results, it is found that the macromolecule causes the clusters of surfactants to be formed at a concentration much lower than the critical micelle concentration. Furthermore, the shape of the clusters tends to be more spherical, which is in line with theory and experiments. From the results, it is learned how a polymer can change the behavior of an amphiphilic molecule. All of the results are in good qualitative agreement with experimental and molecular thermodynamics results. Furthermore, the model predicts network formation between bound clusters at high concentrations of the surfactant.     

Parameterization of a reactive force field using a Monte Carlo algorithm

Parameterization of a molecular dynamics force field is essential in realistically modeling the physicochemical processes involved in a molecular system. This step is often challenging when the equations involved in describing the force field are complicated as well as when the parameters are mostly empirical. ReaxFF is one such reactive force field which uses hundreds of parameters to describe the interactions between atoms. The optimization of the parameters in ReaxFF is done such that the properties predicted by ReaxFF matches with a set of quantum chemical or experimental data. Usually, the optimization of the parameters is done by an inefficient single‐parameter parabolic‐search algorithm. In this study, we use a robust metropolis Monte‐Carlo algorithm with simulated annealing to search for the optimum parameters for the ReaxFF force field in a high‐dimensional parameter space. The optimization is done against a set of quantum chemical data for MgSO₄ hydrates. The optimized force field reproduced the chemical structures, the equations of state, and the water binding curves of MgSO₄ hydrates. The transferability test of the ReaxFF force field shows the extend of transferability for a particular molecular system. This study points out that the ReaxFF force field is not indefinitely transferable. © 2013 Wiley Periodicals, Inc.