Control of Protonated Schiff Base Excited State Decay within Visual Protein Mimics: A Unified Model for Retinal Chromophores

Artificial biomimetic chromophore-protein complexes inspired by natural visual pigments can feature color tunability across the full visible spectrum. However, control of excited state dynamics of the retinal chromophore, which is of paramount importance for technological applications, is lacking due to its complex and subtle photophysics/photochemistry. Here, ultrafast transient absorption spectroscopy and quantum mechanics/molecular mechanics simulations are combined for the study of highly tunable rhodopsin mimics, as compared to retinal chromophores in solution. Conical intersections and transient fluorescent intermediates are identified with atomistic resolution, providing unambiguous assignment of their ultrafast excited state absorption features. The results point out that the electrostatic environment of the chromophore, modified by protein point mutations, affects its excited state properties allowing control of its photophysics with same power of chemical modifications of the chromophore. The complex nature of such fine control is a fundamental knowledge for the design of bio-mimetic opto-electronic and photonic devices.     

A hybrid level set method for modelling detonation and combustion problems in complex geometries

We present an accurate and fast wave tracking method that uses parametric representations of tracked fronts, combined with modifications of level set methods that use narrow bands. Our strategy generates accurate computations of the front curvature and other geometric properties of the front. We introduce data structures that can store discrete representations of the location of the moving fronts and boundaries, as well as the corresponding level set fields, that are designed to reduce computational overhead and memory storage. We present an algorithm we call stack sweeping to efficiently sort and store data that is used to represent orientable fronts. Our implementation features two reciprocal procedures, a forward ‘front parameterization’ that constructs a parameterization of a front given a level set field and a backward ‘field construction’ that constructs an approximation of the signed normal distance to the front, given a parameterized representation of the front. These reciprocal procedures are used to achieve and maintain high spatial accuracy. Close to the front, precise computation of the normal distance is carried out by requiring that displacement vectors from grid points to the front be along a normal direction. For front curves in two dimensions, a cubic interpolation scheme is used, and G ¹ surface parameterization based on triangular patches is used for the three-dimensional implementation to compute the distances from grid points near the front. To demonstrate this new, high accuracy method we present validations and show examples of combustion-like applications that include detonation shock dynamics, material interface motions in a compressible multi-material simulation and the Stephan problem associated with dendrite solidification.     

Combined Chemical Modification and Collision Induced Unfolding Using Native Ion Mobility-Mass Spectrometry Provides Insights into Protein Gas-Phase Structure

Native mass spectrometry is now an important tool in structural biology. Thus, the nature of higher protein structure in the vacuum of the mass spectrometer is an area of significant interest. One of the major goals in the study of gas-phase protein structure is to elucidate the stabilising role of interactions at the level of individual amino acid residues. A strategy combining protein chemical modification together with collision induced unfolding (CIU) was developed and employed to probe the structure of compact protein ions produced by native electrospray ionisation. Tractable chemical modification was used to alter the properties of amino acid residues, and ion mobility-mass spectrometry (IM-MS) utilised to monitor the extent of unfolding as a function of modification. From these data the importance of specific intramolecular interactions for the stability of compact gas-phase protein structure can be inferred. Using this approach, and aided by molecular dynamics simulations, an important stabilising interaction between K6 and H68 in the protein ubiquitin was identified, as was a contact between the N-terminus and E22 in a ubiquitin binding protein UBA2.     

Time evolution of the solvated and conformationally relaxed emissive excited state of the anionic form of salophen,a Schiff base

Salophen is a weakly fluorescent Schiff base which forms emissive co-ordination complexes with Zn²⁺ and Al³⁺. The complex with Al³⁺ is significantly more fluorescent than that with Zn²⁺, presumably because the dimeric complex with Zn²⁺ is associated with additional nonradiative channels. This contention has been put to test, through a careful investigation of excited state dynamics of the anionic form of salophen (Sal²⁻), which is the form in which the ligand exists in the complexes. The emissive excited state of the anion (Sal²⁻) has been found to be solvated and conformationally relaxed, over tens of picosecond. It is significantly more fluorescent than the neutral compound, with fluorescence lifetime that is longer by almost two orders of magnitude. Fluorescence lifetime of the anion is in fact longer than that of the complex with Zn²⁺ and slightly less than that of the complex with Al³⁺. So, the earlier hypothesis about additional nonradiative deactivation pathways in the Zn²⁺ complex gains credence from the present study.     

Nonequilibrium molecular dynamics simulation of coupling between nanoparticles and base-fluid in a nanofluid

The intent of this study is to examine nonequilibrium heat transfer in a copper-argon nanofluid by molecular dynamics simulation. Two different methods, the physical definition method and the curve fitting method, are introduced to calculate the coupling factor between nanoparticles and base fluid. The results show that the coupling factors obtained by these two methods are consistent. The coupling factor is proportional to the volume fraction of the nanoparticle and inversely proportional to nanoparticle diameter. In the temperature range of 90-200 K, the coupling factor is not affected by temperature. The nanoparticle aggregation results in a decrease of the coupling factor.     

Discontinuous Galerkin methods on graphics processing units for nonlinear hyperbolic conservation laws

We present a novel implementation of the modal DG method for hyperbolic conservation laws in two dimensions on graphics processing units (GPUs) using NVIDIA's Compute Unified Device Architecture. Both flexible and highly accurate, DG methods accommodate parallel architectures well as their discontinuous nature produces element‐local approximations. High‐performance scientific computing suits GPUs well, as these powerful, massively parallel, cost‐effective devices have recently included support for double‐precision floating‐point numbers. Computed examples for Euler equations over unstructured triangle meshes demonstrate the effectiveness of our implementation on an NVIDIA GTX 580 device. Profiling of our method reveals performance comparable with an existing nodal DG‐GPU implementation for linear problems. Copyright © 2014 John Wiley & Sons, Ltd.     

也谈《高分子化学》课程教学的工科特色

《高分子化学》课程是大部分工科化工、材料类专业的必修课程,如何在工科专业高分子化学课程教学中体现工科特色,成为大家关注的热点.针对什么是工科特色,提出了本人的见解.并就如何在教学过程中体现工科特色介绍了本人的探索与尝试.     

金钗石斛中生物碱提取的动力学分析

将金钗石斛用氨水浸润后,以氯仿为溶剂,在不同液固比、不同提取时间和不同提取温度下提取生物碱,以Fick第二定律为依据,以提取生物碱质量浓度为检测指标,求解提取动力学的表观传质速率方程、速率常数k、相对萃余率和表观活化能Ea等数值,建立金钗石斛生物碱提取过程的动力学模型.结果显示:在液固比为60,提取温度为60℃,提取时间为90 min时,所提取的生物碱质量浓度较高,金钗石斛生物碱提取过程的动力学基本符合一级动力学方程,在不同影响因素下,表观传质速率ln[C_∞/(C_∞-C_0)]、相对萃余率与时间t均有比较好的线性关系,提取动力学方程的活化能Ea为55.075 k J/mol.由此知金钗石斛生物碱提取过程的关键控制步骤为溶质的内扩散步骤.