One-dimensional free-energy profiles of complex systems: progress variables that preserve the barriers

We show that the balanced minimum-cut procedure introduced in PNAS 2004, 101, 14766 can be reinterpreted as a method for solving the constrained optimization problem of finding the minimum cut among the cuts with a particular value of an additive function of the nodes on either side of the cut. Such an additive function (e.g., the partition function of the reactant region) can be used as a progress coordinate to determine a one-dimensional profile (FEP) of the free-energy surface of the protein-folding reaction as well as other complex reactions. The algorithm is based on the network (obtained from an equilibrium molecular dynamics simulation) that represents the calculated reaction behavior. The resulting FEP gives the exact values of the free energy as a function of the progress coordinate; i.e., at each value of the progress coordinate, the profile is obtained from the surface with the minimal partition function among the surfaces that divide the full free-energy surface between two chosen end points. In many cases, the balanced minimum-cut procedure gives results for only a limited set of points. An approximate method based on p(fold) is shown to provide the profile for a more complete set of values of the progress coordinate. Applications of the approach to model problems and to realistic systems (beta-hairpin of protein G, LJ38 cluster) are presented.     

Adaptive umbrella sampling of the potential energy: modified updating procedure of the umbrella potential and application to peptide folding

Adaptive umbrella sampling of the potential energy is used as a search method to determine the structures and thermodynamics of peptides in solution. It leads to uniform sampling of the potential energy, so as to combine sampling of low-energy conformations that dominate the properties of the system at room temperature with sampling of high-energy conformations that are important for transitions between different minima. A modification of the procedure for updating the umbrella potential is introduced to increase the number of transitions between folded and unfolded conformations. The method does not depend on assumptions about the geometry of the native state. Two peptides with 12 and 13 residues, respectively, are studied using the CHARMM polar-hydrogen energy function and the analytical continuum solvent potential for treatment of solvation. In the original adaptive umbrella sampling simulations of the two peptides, two and six transitions occur between folded and unfolded conformations, respectively, over a simulation time of 10 ns. The modification increases the number of transitions to 6 and 12, respectively, in the same simulation time. The precision of estimates of the average effective energy of the system as a function of temperature and of the contributions to the average effective energy of folded conformations obtained with the adaptive methods is discussed. Received: 11 July 1998 / Accepted: 22 September 1998 / Published online: 17 December 1998     

Multidimensional adaptive umbrella sampling: Applications to main chain and side chain peptide conformations

A new adaptive umbrella sampling technique for molecular dynamics simulations is described. The high efficiency of the technique renders multidimensional adaptive umbrella sampling possible and thereby enables uniform sampling of the conformational space spanned by several degrees of freedom. The efficiency is achieved by using the weighted histogram analysis method to combine the results from different simulations, by a suitable extrapolation scheme to define the umbrella potential for regions that have not been sampled, and by a criterion to identify simulations during which the system was not in equilibrium. The technique is applied to two test systems, the alanine dipeptide and the threonine dipeptide, to sample the configurational space spanned by one or two dihedral angles. The umbrella potentials applied at the end of each adaptive umbrella sampling run are equal to the negative of the corresponding potentials of mean force. The trajectories obtained in the simulations can be used to calculate dynamical variables that are of interest. An example is the distribution of the distance between the HN and the Hβ proton that can be important for the interpretation of NMR experiments. Factors influencing the accuracy of the calculated quantities are discussed. © 1997 John Wiley & Sons, Inc. J Comput Chem 18 : 1450–1462, 1997     

Conformational sampling via a self-regulating effective energy surface

The difficulty of efficiently sampling the phase space of complex systems with rough energy surfaces is well known. Typical solutions to the problem involve accelerating the crossing of barriers, but such methods often have the secondary problem that the low-energy states of interest are inadequately sampled, unless the parameters of the search algorithm are modified as the system evolves. A method is presented to improve the sampling with particular emphasis on the low-energy conformations, which make the most important contributions to the thermodynamics of the system. The algorithm proposed here samples the details of the minima, while easily surmounting barriers. This is achieved by introducing a self-regulating sampling variable which depends on the current state of the system. Two replicas of the system are introduced and the sampling variable is treated as a particle coupled to the physical system. The method is illustrated with a simple model system and is applied to the realistic example of barrier crossing in a protein-ligand complex.     

基于箭形累积损伤的裂纹尖端力学:奇异性分级和多尺度分段

在适度的空间和时间尺度组合下,裂纹既可在几个月中蠕变几个纳米,也能在几秒钟内扩展10km.虽然裂纹的尖端没有实际的质量,但是它能通过激活周围的物质而处于高能量状态.依赖于材料的损伤方向,激活质量的减少和增加可发生在尺度转变之前或之后.每个尺度区的分段阈值被假定为与裂纹尖端速度的平方a~2和激活质量密度M的乘积有关:W=M_(↓↑)a_(↑↓)~2和D=M~(↓↑)a_(↑↓)~2.W和D分别被称为直接吸收和自耗散能量密度.正如下标/上标符号所示,激活的质量密度M_(↓↑)和M~(↓↑)与裂纹尖端速度a变化趋势相反,既可增加也可减少.a~2和M的互补效应隐含着常用于宇宙物理学建模的膨胀和/或收缩的物理过程.在用于尺度敏感的裂纹尖端的行为时,激活的质量密度有相同的解释.分段时的多尺度可以由…皮观、纳观、微观和宏观…组成.因此,形象地说,材料损伤过程可以通过裂纹扩展过程中非均匀的总体和局部能量的传递来模拟.疲劳裂纹扩展引起的材料损伤被用来阐释由大到小和由慢到快的尺度/时间序,热力学中的冷→热和有序→无序转换.这一过程正巧与宇宙演化的箭形方向相反,宇宙演化遵循小→大和快→慢,而热力学相反,遵循热→冷和无序→有序.为了表示由损伤萌生所造成的类裂缝型缺陷的不均匀性,提出了一个被称为裂纹尖端力学(crack tip mechanics,CTM)的新模式.涉及的范围是模拟原子列之间的界面裂纹或连续体中分叉的切口.假如需要的话,尺寸和时间的范围可以复盖从皮观到宏观甚至更大.虽然采用疲劳裂纹来说明CTM的基本原理,在宇宙物理学背景中与直接吸收和自耗散相关的膨胀和收缩的情况可以描述裂纹周围激活质量的行为,它们可看为能量的汇或源.奇异性被用来捕获能量的源或汇的特性,物理上,两者作为界面的一部分,从数学上看则是不连续的线的一部分.能量从一种形式变为另一种形式取决于能量吸收或耗散的箭形损伤时间,这之中牵涉到尺度分段和奇异性强度的联合应用.材料组分随时间的劣化是根据指定的设计寿命导出的,从而使材料的响应与加载率的时间历史匹配.2024-T3铝板的皮观/纳观/微观/宏观开裂模型用来说明什么地方可以增加结构的寿命部分.皮观/纳观/微观/宏观/结构系统的性能随时间劣化可以用9个尺度转变物理参数来描述:纳观/微观区有3个(μ_(na/mi)~*,σ_(na/mi)~*,d_(na/mi)~*),微观/宏观区有3个(μ_(mi/ma)~*,σ_(mi/ma)~*,d_(mi/ma)~*),皮观/纳观区有3个(μ_(pi/na)~*,σ_(pi/na)~*,d_(pi/na)~*).下标pi,na,mi,ma和struc分别表示皮观、纳观、微观、宏观和结构.只要知道两个相连的尺度敏感参数,在较低尺度的时间相关的局部物理参数就完成了分析连续体的形式论,虽然它们并不需要用实验来知道.更具体地说,根据皮观→纳观→微观→宏观分别有1.25/1.00/0.75/0.50的λ奇异性强度,皮观裂纹、纳观裂纹、微观裂纹和宏观裂纹的转变特征是从时间箭形的指定的寿命预期来确定的.附加的0.25强度的奇异性可用于结构元件.回想起来,λ=0.5相应于断裂力学中的应力分量与r~(0.5)成反比,r是与宏观裂纹尖端的距离.微观裂纹、纳观裂纹和皮观裂纹分别赋予r~(-0.75),r~(-1.0),r~(-1.25)的奇异性.箭形时间(以年为单位)取决于问题的定义.设备的关键部件可用1.5~±/2.5~±/3.5~±/5.5~±寿命分布和总寿命为13~±年(a)的皮观/纳观/微观/宏观尺度来设计运行.上标±表示多于或少于实际运行的时间.累进损伤被假定为发生在皮观→纳观→微观→宏观方向.同样的方案用于20年总寿命的2024-T3铝板的疲劳损伤,按照1.5~±/2.5~±/3.5~±/5.5~±/7.0~±的方式将它的寿命分布在皮观、纳观、微观、宏观和结构的尺度上,这样的指定只是满足在每个尺度范围内损伤内部材料结构所用的能量匹配,因此可以强制执行在总寿命的跨度内精确的时间相关的材料性能劣化过程.     

Triosephosphate isomerase: a theoretical comparison of alternative pathways.

Three mechanisms proposed for the triosephosphate isomerase (TIM) catalyzed reactions were studied with the QM/MM approach using B3LYP/6-31+G(d,p) as the QM method. The two pathways that involve an enediol species were found to give similar values for the barriers and the calculated rates are in satisfactory agreement with experiment. By contrast, the mechanism that involves intramolecular proton transfer in the enediolate was found to be energetically unfavorable due to electrostatic interactions with His 95, a conserved residue in TIM from different organisms. A perturbation analysis was used to determine the residues that make the major contribution to catalysis.     

On the electric current from electrodes in a magnetized semiconductor film

The problem on the electric current from electrodes in a magnetizedsemiconductor film is reduced to the skew derivative problemfor the Laplace equation outside cuts in a plane. The problemfor the Laplace equation is studied under different conditionsat infinity, which have a certain physical meaning. With thehelp of potential theory, the skew derivative problem is reducedto a Fredholm integral equation of the second kind, which isuniquely solvable. The Neumann problem for the Laplace equationin the exterior of cuts in a plane is a particular case of ourproblem.