Generalised expressions for the association and dissociation rate constants of molecules with multiple binding sites

ABSTRACT

Many proteins exhibit multiple binding patches. A patch may harbour a key chemical modification site, but may also simply act as a trap for the binding to another site. Here we consider the scenario in which one molecule (enzyme) binds another molecule (substrate) which contains two sites. We present microscopic expressions for the rate at which the enzyme binds to a particular site on the substrate, both for the scenario in which the enzyme directly binds the site without first visiting the other site, and for the case in which it may visit the other site an arbitrary number of times before binding to the site of interest. We also present the expressions for the corresponding dissociation reactions. These expressions can be used to compute in a single rare-event simulation of the dissociation pathway not only both the intrinsic and effective dissociation rate constants but also both association rate constants.     

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.     

Nd:GGG晶体荧光寿命的测试

针对Nd:GGG激光器,介绍了荧光寿命测试原理,设计了低频窄脉宽荧光寿命测试系统.该系统由光源、光路系统、驱动电路和探测系统等几部分组成.利用脉冲取样技术测试了Nd:GGG晶体的荧光寿命约为250μs左右.     

场分析法与阻抗叠加方法在速调管输出腔间隙阻抗计算中的应用

 从分析速调管输出回路的电磁场分量入手,结合微波电路理论,提出了计算速调管输出回路间隙阻抗的场分析法。对于在谐振模式交叠频带上,群聚电子束电流同时与各模式的阻抗相作用,总阻抗是各模式阻抗的代数叠加的情况,提出了阻抗叠加方法。该方法原则上可求解任意给定间隙电阻所对应的间隙电抗值。计算表明,场分析法与等效间隙阻抗法计算结果最大相对误差为1.5％,阻抗叠加方法计算结果与冷测数据最大相对误差为10％。分析表明,多个谐振模式的引进是速调管输出腔加载滤波器展宽频带的物理实质。     

电容量及损耗角的一种测量方法

介绍了在微机控制的自动测量装置中采用的双极性电容器的测试方法。这种方法用反相运算放大器微分电路获得与电容器相关的两个工频电压,并通过对它们数字化输入微机内存,最后通过对数字化后的两个周期信号进行处理求得电容量和损耗角正切。     

Radiation damping in closed expanding universes

The dynamics of a coupled model (harmonic oscillator-relativistic scalar field) in Conformal Robertson-Walker (k = +1) spacetimes is investigated. The exact radiation-reaction equation of the source-including the retarded radiation terms due to the closed space geometry – is obtained and analyzed. A suitable family of Lyapunov functions is constructed to show that, if the spacetime expands monotonely, then the source's energy damps. A numerical simulation of this equation for expanding Universes, with and without Future Event Horizon, is performed.     

掺杂对碳纳米管拉曼光谱及场发射性能的影响

采用高温热解法在860℃分别制备出了镓、氮以及硼和氮掺杂的碳纳米管,提纯后利用丝网印刷工艺分别将它们制备成薄膜,并测试了它们的拉曼光谱与场发射性能。测试结果表明,掺杂纳米管的缺陷密集度比纯碳纳米管明显增大,而它们的场致电子发射性能则与掺杂元素的性质密切相关。镓和氮掺杂的纳米管均具有非常优异的场发射性能,而硼和氮共掺杂的纳米管的场发射性能很差。掺杂引起碳纳米管费米能级附近能态密度的变化及功函数的降低是其具有优异场致电子发射性能的主要原因。     

一种改进的计算探测器校正因子的相关抽样方法

对于小尺寸探测器处于大块介质的情形, 在探测器的校正因子的Monte Carlo模拟中, 存在两个难题: 一是由于探测器尺寸很小粒子难以到达探测器并发生碰撞; 二是两个随机变量比值难以达到要求精度. 本文使用经过改进的粒子碰撞自动重要抽样方法, 再结合相关抽样方法, 解决了这两个难题, 并在MCNP-4C程序平台上加以实现. 除了粒子碰撞自动重要抽样以外, 还选用了其他3种方法: 直接模拟、区域分裂、强迫碰撞+Dxtran球分别与相关抽样方法结合, 对一个简化的探测器校正因子计算模型进行了计算. 实际计算结果表明, 相关抽样方法无论与哪种方法结合, 都起到了提高相关量计算效率的作用; 而它与粒子碰撞自动重要抽样结合, 比其他方法具有明显的优越性.     

Field emission characteristics of screen-printed carbon nanotubes cold cathode by hydrogen plasma treatment

Selective plasma etching and hydrogen plasma treatment were introduced in turn to improve field emission characteristics of screen-printed carbon nanotubes (CNTs) cold cathode, which was prepared by using slurry of mixture of multi-wall CNTs, organic vehicles and inorganic binder, i.e. silicon dioxide sol. The results show that selective plasma etching process could effectively remove parts of surface inorganic vehicle (SiO₂) layer and expose more smooth and clean CNTs on cathode surface, which could significantly decrease the operating field of CNTs cathode. There are some nanoparticles emerging on the out of CNTs wall after hydrogen plasma treatment, which are equivalent to increase field emission point of cathode. At the same time, these nanoparticles can increase the local electric field of CNTs, which can decrease operating voltage of CNTs cathode and improve uniformity field emission.     

Field history dependence of nonlinear dielectric properties of Ba0.6Sr0.4TiO3 ceramics under bias electric field: Polarization behavior of polar nano-regions

Nonlinear dielectric properties of Ba_0.6Sr_0.4TiO₃ ceramics prepared by citrate method were investigated under bias electric field with respect to field history. X-ray diffraction analysis and temperature dependence of the dielectric constant (ε_r) confirmed a macroscopically paraelectric state for the specimen at room temperature. A slim polarization versus electric field (P-E) hysteresis loop of the specimen at room temperature indicated the existence of polar nano-regions (PNRs) superimposed on the paraelectric background. The nonlinear dielectric properties in continuous cycles of bias field sweep displayed a strong sensitivity to the field history. This phenomenon was qualitatively explained in terms of an irreversible polarization evolution of the PNRs under the bias fields. A considerable decline of the tunability with the cycle number suggests an appreciable contribution of the PNRs to the dielectric nonlinearity. The polarization and size of the PNRs were determined by fitting the dielectric constants to a multipolarization mechanism model.