Thermodynamic properties of solvated peptides from selective integrated tempering sampling with a new weighting factor estimation algorithm

Conformational sampling under rugged energy landscape is always a challenge in computer simulations. The recently developed integrated tempering sampling, together with its selective variant (SITS), emerges to be a powerful tool in exploring the free energy landscape or functional motions of various systems. The estimation of weighting factors constitutes a critical step in these methods and requires accurate calculation of partition function ratio between different thermodynamic states. In this work, we propose a new adaptive update algorithm to compute the weighting factors based on the weighted histogram analysis method (WHAM). The adaptive-WHAM algorithm with SITS is then applied to study the thermodynamic properties of several representative peptide systems solvated in an explicit water box. The performance of the new algorithm is validated in simulations of these solvated peptide systems. We anticipate more applications of this coupled optimisation and production algorithm to other complicated systems such as the biochemical reactions in solution.     

用李代数方法构造四原子分子的势能面

把李代数方法得到的四原子分子的代数Hamiltonian，利用相干态经典化之后并找到一个新的变换，将分子的键角引入，而得到四原子分子的势能面.由该势能面计算得到的解离能与力常数与其他方法给出的一致.     

非均匀外力对粗粒化DNA穿孔行为影响的模拟研究

通过建立DNA高分子的粗粒化模型,采用分子动力学方法模拟其穿孔行为,研究了不同的孔内非均匀外力对DNA高分子穿孔的影响.外力及高分子链内部势能在分子水平下对单体的综合作用很复杂,某些条件穿孔过程会产生后面粒子超过前面粒子而使高分子链堵塞在孔内的情况.研究还发现,穿孔行为是否成功与孔口力的大小有关,在成功穿孔的情况下,非均匀外力相比于恒力情况穿孔时间至少减少了1/2.这些结果对理解DNA复杂的穿孔机理提供了新的视角.     

Saddle points of the potential energy surface for HCCF determined by an algebraic approach

The potential energy surface of the tetratomic molecule HCCF is determined by the U(4) algebraic method. The combination coefficients in the Hamiltonian are gotten from fitting the spectroscopic data. The molecular properties, such as, force constants and dissociation energies, are obtained in terms of the potential energy surface. A saddle point is also derived.Received: 17 November 2003, Published online: 9 March 2004PACS: 02.20.Sv Lie algebras of Lie groups - 34.20.Cf Interatomic potentials and forces     

表面增强拉曼光谱技术检测新型冠状病毒刺突蛋白

开发具有高灵敏度、高准确性的新型冠状病毒（SARS-CoV-2）快速检测技术对疫情防控具有重要作用。本文利用表面增强拉曼光谱（SERS）技术对人体唾液中的痕量SARS-CoV-2病毒刺突蛋白（S蛋白）进行了检测。结果表明,含S蛋白的唾液样本与原始唾液样本的拉曼光谱具有显著区别,含S蛋白的唾液样本谱图中可清晰观察到属于S蛋白的拉曼谱线。该结果为后续SERS技术在SARS-CoV-2病毒快速检测方面的应用奠定了坚实基础。

     

Magnetohydrodynamic flow and heat transfer of a hybrid nanofluid over a rotating disk by considering Arrhenius energy

This research work explores the effect of hybrid nanoparticles on the flow over a rotating disk by using an activation energy model. Here, we considered molybdenum disulfide and ferro sulfate as nanoparticles suspended in base fluid water. The magnetic field is pragmatic normal to the hybrid nanofluid flow direction. The derived nonlinear ordinary differential equations are nondimensionalized and worked out numerically with the help of Maple software by the RKF-45method. The scientific results for a non-dimensionalized equation are presented for both nanoparticle and hybrid nanoparticle case. Accoutrements of various predominant restrictions on flow and thermal fields are scanned. Computation estimation for friction factor, local Nusselt number and Sherwood number are also executed. Results reveal that the reduction of the heat transfer rate is greater in hybrid nanoparticles when compared to nanoparticles for increasing values of Eckert Number and the thermal field enhances for the enhanced values of volume fraction.     

一个保守力作的功能等于势能的减少吗

通过实例说明一个保守力作的功,在一般情况下并不等于势能的减少,一个对保守力作用功才等于势能的减少。     

Equilibrium folding and unfolding dynamics to reveal detailed free energy landscape of src SH3 protein by magnetic tweezers

Src SH3 protein domain is a typical two-state protein which has been confirmed by research of denaturant-induced unfolding dynamics. Force spectroscopy experiments by optical tweezers and atomic force microscopy have measured the force-dependent unfolding rates with different kinds of pulling geometry. However, the equilibrium folding and unfolding dynamics at constant forces has not been reported. Here, using stable magnetic tweezers, we performed equilibrium folding and unfolding dynamic measurement and force-jump measurement of src SH3 domain with tethering points at its N-and C-termini. From the obtained force-dependent transition rates, a detailed two-state free energy landscape of src SH3 protein is constructed with quantitative information of folding free energy, transition state barrier height and position,which exemplifies the capability of magnetic tweezers to study protein folding and unfolding dynamics.     

Pt(110)表面自吸附原子能量和力的改进分析型嵌入原子法分析

采用改进分析型嵌入原子法计算了Pt(110)表面自吸附原子的能量和法向力.当Pt吸附原子位于Pt(110)表面第一层原子的二重对称洞位上0.11nm时最稳定.Pt吸附原子的最佳迁移路径是由一个二重对称洞位沿密排方向迁移到最近邻的另一个二重对称洞位.在吸附原子远离表面的过程中，将依次经过排斥、过渡和吸引等三个区域.在排斥区和过渡区，由于吸附原子与表面原子间强的相互作用势，吸附原子的能量和法向力的形貌图均为(110)面原子排列的复形，与对势理论和嵌入原子法得到的结果一致.在吸引区，由于多体相互作用及晶体中原子 关键词： 金属表面 自吸附 能量 力     

离子束修形中光学元件表面热量沉积数值模拟

根据Sigmund溅射能量沉积理论建立了低能离子入射光学元件引起的能量扰动层厚度模型．理论推导了离子束倾斜入射时光学元件表面的束流密度,并建立了低能离子束对光学元件的热量沉积模型．采用MonteCarlo方法模拟了低能离子与熔石英光学表面的相互作用．分析了离子能量、离子类型、入射角度等参数对光学元件热量沉积和扰动层深度的影响规律．以离子束沉积在工件的能量作为热源,采用有限元分析软件ANSYS模拟了离子束入射工件的温度场分布、温度梯度场分布和温度应力分布．入射表面温度和热梯度呈高斯分布,束斑中心最高并向工件边缘逐渐减小．入射表面束斑区域受热膨胀,其膨胀受到外环区域的制约,从中心区域到大约束斑半峰值半径的区域,所受环向应力为压应力,在大致束斑半峰值半径以外区域为拉应力．     

Accurate double many-body expansion potential energy surface of HS_2(A~2A') by scaling the external correlation

A globally accurate single-sheeted double many-body expansion potential energy surface is reported for the first excited state of HS_2 by fitting the accurate ab initio energies, which are calculated at the multireference configuration interaction level with the aug-cc-pVQZ basis set. By using the double many-body expansion-scaled external correlation method,such calculated ab initio energies are then slightly corrected by scaling their dynamical correlation. A grid of 2767 ab initio energies is used in the least-square fitting procedure with the total root-mean square deviation being 1.406 kcal · mol~(-1).The topographical features of the HS_2(A_2A') global potential energy surface are examined in detail. The attributes of the stationary points are presented and compared with the corresponding ab initio results as well as experimental and other theoretical data, showing good agreement. The resulting potential energy surface of HS_2(A_2A') can be used as a building block for constructing the global potential energy surfaces of larger S/H molecular systems and recommended for dynamic studies on the title molecular system.     

Semiclassical line broadening calculations,using an ab initio potential energy surface,in Q‐branch and S‐branch of N2 perturbed by H2

In order to improve the accuracy of Raman combustion diagnostics, the broadening coefficients of N₂ perturbed by H₂ for Q‐branch and S‐branch have been calculated by the semiclassical Robert–Bonamy model using an ab initio potential energy surface. The calculations have been performed for a large range of temperatures (from 77 to 800 K) and J rotational quantum numbers (from 0 to 60). This paper shows that our results and their temperature dependence are in good agreement with earlier published experimental and theoretical data. Moreover, our results improve the semiclassical calculations made earlier with an adapted analytical potential. The results, obtained at high temperatures and for a large range of rotational quantum numbers, are presented in order to be implemented for optical diagnostics in combustion media. Copyright © 2012 John Wiley & Sons, Ltd.     

Effects of Cu2−xS phase removal on surface potential of Cu2ZnSnS4 thin-films grown by electroplating

Cu₂ZnSnS₄ (CZTS) has an optical band gap of 1.4–1.5 eV, which is similar to that of Cu(In,Ga)Se₂ (CIGS), and a high absorption coefficient (>10⁴ cm⁻¹) in the visible light region. In previous reports, CIGS thin-film solar cells have been shown to improve the performance of the device since the secondary phase is removed by Potassium cyanide (KCN) etching treatment. Therefore, in this study we applied a KCN etching treatment on CZTS and measured the effects. We confirmed the removal of Cu_2−xS via Kelvin probe force microscopy (KPFM) and Raman scattering spectroscopy. The effects of the experiment indicate that we can define with precision the location of the secondary phases, and therefore the control of the secondary phases will be easier and more efficient. Such capabilities could improve the solar cell performance of CZTS thin-films.     

182Os 核yrast带相继SU(3)–U(5)–SU(3)结构相变势能曲面的一种可能理解

基于联合实施微观相互作用玻色子模型的最大F旋方案 (sdIBM-F_max)与γ射线能量-自旋曲线 (γ-ray energy over spin curves, E-GOS)方案, 成功描述了¹⁸²Os核yrast带相继的SU(3)–U(5)–SU(3)结构相变, 由于缺少直观解释而显得抽象. 本文借助微观sdIBM-F_max的微观参数与Bohr哈密顿量的势能曲面方程之间存在的泛函关系, 几何地给出了对这种相继相变途径的另外一种可能理解; 并阐述了在完全变形核的高角动量态中, 由于量子效应在高激发态与低激发态之间生成高简并的临界区, 提供了γ振动能量会变得低于转动能量的一个可能途径, 从而实现了SU(3)–U(5)的相变. 关键词： yrast带结构演化 势能曲面 相变临界区 182Os核')" href="#">¹⁸²Os核