CAREER: Development of Non-Additive Lipid Force Fields and Application to the Study of Charged Amino Acid Residues in Lipid Bilayers and the Role of Bilayer-Resident Water

智力优势 活细胞有一个内部和一个外部，由称为细胞膜的屏障隔开，主要由称为脂质的基本单位组成。在水中快乐（能量稳定）的分子（如盐、离子、极性分子）在膜状环境中并不总是快乐的。 然而，令人惊讶的是，在膜中发现了许多亲水分子，或者已知它们很容易穿过膜环境。观察到细胞穿透肽容易进入细胞。由于喜水分子似乎存在于细胞膜内并通过细胞膜转移，因此很自然地认为水是沿着的。水在这些过程中发挥着重要作用。由于不可能通过实验室实验看到单个水分子，因此将使用计算机程序来执行所谓的分子模拟。这些计算方法结合了生物分子如何相互作用的物理学的数学描述，遵循单个分子在时间和空间中的运动。这使研究人员能够探索与细胞膜（双层）相关的水在极性和带电分子通过该环境转移中的作用。这个观点是在原子和分子水平上！ 新的方法将被用来描述水和渗透分子的不同分子特性，因为它们通过截然不同的环境移动。这项研究将解决水和脂质在膜中的相互作用。具体地说，渗透分子局部环境中存在的水是否支持膜的结构变化，使分子稳定在“油性”脂质区域？更广泛地说，理解水在不同环境中的作用对许多科学和技术背景都有影响（水介导的纳米粒子自组装、胶体悬浮液及其在环境中的作用等），从而促进我们对这种普遍存在的溶剂及其在不同科学和技术重要化学环境中的行为的全球理解。 这些新的方法在新的计算机硬件上的应用，如图形处理单元（GPU），现在正在成为可行的商品高性能计算替代日常计算将继续下去。更广泛的影响受定量和定性科学学科之间的合作，以促进我们对基本生物物理和生物化学过程的理解的不可避免的当前和未来需求的激励，将确立两个教育/外联目标。1）。由一名大学教授和两名资深教师组成的多学科团队（化学/物理和生物）将介绍纽瓦克高中的学生（NHS;服务于少数民族学生和科学，技术和工程中代表性不足的群体的大量人口），以介绍计算化学课程，将强调多学科方法的哲学，结合技能集，工具，以及化学、生物学、物理学、数学和计算机科学领域的知识，以理解基本的生物物理现象。这将使学生接触到在学术界和工业界广泛使用的实用计算机工具和技能。 2）。为了支持特拉华州大学本科化学和生物化学学生的数学准备，并激发学生对生物物理，化学物理和计算科学等领域研究的兴趣，将开发一门介绍性计算化学课程，使用最先进的计算机和程序，专注于化学数学，解决化学性质的问题，并为学生准备物理化学课程的数学严谨性。这种额外的准备和机会，为化学学生提高他们的基本数学技能将使物理化学一个不那么繁重，更丰富（也许是有趣）的经验，为学生。 项目目标是在职业生涯的早期阶段提高学生的定量推理能力，从而建立一个坚实的平台，以追求与未来社会需求相关的众多研究途径。

Intellectual Merit Living cells have an inside and an outside, separated by a barrier called the cell membrane, primarily made of fundamental units called lipids. Molecules (such as salts, ions, polar molecules) that are happy (energetically stable) in water are not always happy in a membrane-like environment. Surprisingly, however, numerous water-loving molecules are found in the membrane or are known to cross the membrane environment quite easily. Cell penetrating peptides are observed to readily enter cells. Since water-loving molecules appear to reside within and transfer through the cell membrane, it is natural to think that water goes along for the ride. Water has an important role in these processes. Since it is impossible to see individual water molecules with laboratory experiments, computer programs will be used to perform what are known as molecular simulations. These computational methods, incorporating mathematical descriptions of the physics of how biological molecules interact with one another, follow the motions of individual molecules in time and space. This allows researchers to explore the role of water associated with cell membranes (bilayers) in the transfer of polar and charged molecules through this environment. The view is at the atomic and molecular level! Novel methods will be used that have been developed to describe the varying molecular properties of water and permeating molecules as they move through sharply different environments. The research will address the interaction between water and lipids in the membrane. Specifically, does the water present in the local environment of the permeating molecule support structural changes of the membrane that stabilize the molecule in the "oily" lipid region? More broadly, understanding the role of water in differing environments has implications in numerous scientific and technological contexts (water-mediated self-assembly of nanoparticles, colloidal suspensions and their role in the environment, etc.), thus furthering our global understanding of this ubiquitous solvent and its behavior across different scientifically and technologically important chemical environments. Application of these novel methods on new computer hardware such as Graphical Processing Units (GPU's) that are now becoming viable commodity high-performance computing alternatives for routine computing will be continued.Broader ImpactsMotivated by the inescapable current and future requirement for cooperation between the quantitative and qualitative scientific disciplines to further our understanding of fundamental biophysical and biochemical processes, two educational/outreach goals will be established. 1). A multi-disciplinary team consisting of a university professor and two veteran teachers (of chemistry/physics and biology) will introduce students at Newark High School (NHS; which serves a substantial population of minority students and groups underrepresented in science, technology, and engineering) to an introductory computational chemistry course that will emphasize a philosophy of multi-disciplinary approaches, combining the skill sets, tools, and knowledge of the fields of chemistry, biology, physics, math, and computer science, to understanding fundamental biophysical phenomena. This will expose students to practical computer tools and skills widely used in academia and industry. 2). To support the mathematics preparedness of undergraduate chemistry and biochemistry students at the University of Delaware, and to spark greater student interest in the pursuit of research in such fields as biophysics, chemical physics, and computational sciences, an introductory computational chemistry course will be developed, using state-of-the-art computers and programs, focusing on mathematics of chemistry to solve problems of a chemical nature and to prepare students for the mathematical rigor of Physical Chemistry courses. Such extra preparation and opportunities for chemistry students to sharpen their basic math skills will make Physical Chemistry a less burdensome, more enriching (and perhaps fun) experience for students. Project goals serve to increase students' quantitative reasoning skills at an early point in their careers, thus establishing a firm platform from which to pursue numerous avenues of research relevant to future societal needs.