Understanding the growth mechanism of L-cystine crystal using three dimentional Monte-Carlo simulation_ Zulaikha Alharthi

These are the supplementary videos of Zulaikha's thesis entitled: understanding the growth mechanism of L-cystine crystals vis three-dimensional Monte-Carlo simulation. The objective of these materials is to give more insight into the details of the growth mechanism of L-cystine crystals using insitu AFM microscopy and CrystalGrower package. This study investigated the mechanism by which L-cystine imposter (L-cystine dimethyl ester, L-cystine methyl ester and N-acetyl L-cysteine) inhibit the crystal grwoth. The changes in crystal morphology, as well as polymorph, was interpreted using kinetic Monte-Carlo simulation. The changes in the crystal habit from hexagonal disc to hexagon prism is proved by poisoning certain sites in ab plane where the ring-like conformation of H-bonding was disrupted. The changes on the crystal surface were investigated using AFM. The study deciphers the influence of stress around the dislocation core in both growth and dissolution processes. The growth of L-cystine was followed using insitu AFM. The presence of two different types of dislocations on the surface and their importance on the growth, the different types of stress and the details of dissolution spirals are examples of the results obtained via AFM. These results are explained using CrystalGrower and extended to kinetic perspectives using simulation output. Like molecular crystals, L-cystine is characterised by anisotropic bonding that shows a couple of interesting features on the crystal surface. These were detailed using AFM. These are finger-like structures, islands amidst growing layers, composite spirals, multi-spirals and a sequence of steps colliding and annihilating each other. The finger features were successfully simulated and explained in view of growth anisotropy in the main growth directions of the crystal.本数据集为祖莱卡（Zulaikha）博士论文的补充视频，论文主题为基于三维蒙特卡洛（Monte-Carlo）模拟解析L-胱氨酸晶体的生长机制。本补充材料旨在通过原位原子力显微镜（Atomic Force Microscopy, AFM）与CrystalGrower工具包，更深入地揭示L-胱氨酸晶体生长机制的细节。 本研究探究了L-胱氨酸类似物（L-胱氨酸二甲酯、L-胱氨酸甲酯与N-乙酰基-L-半胱氨酸）抑制晶体生长的机制，并通过动力学蒙特卡洛模拟阐释了晶体形貌与晶型的变化规律。研究通过毒化ab晶面上的部分位点（破坏了氢键环状构象），证实了晶体生长习性从六角盘状向六角棱柱状的转变，并借助原子力显微镜观测了晶体表面的形貌变化。 本研究解析了位错核心周围的应力对晶体生长与溶解过程的影响，通过原位原子力显微镜实时追踪了L-胱氨酸晶体的生长过程。通过原子力显微镜获得的研究结果包括：晶体表面存在的两类不同位错及其对晶体生长的作用、不同类型的应力分布，以及溶解螺旋的详细特征等。研究借助CrystalGrower工具包对上述结果进行了解释，并通过模拟结果将分析拓展至动力学维度。 与分子晶体类似，L-胱氨酸具有各向异性的键合特性，其晶体表面呈现出多种有趣的表面特征，本研究通过原子力显微镜对这些特征进行了详细表征，包括指状结构、生长层间的岛状结构、复合螺旋、多重螺旋，以及台阶相互碰撞并湮灭的一系列过程。研究成功模拟了指状结构，并基于晶体主生长方向的生长各向异性对其进行了合理解释。