Philadelphia 2012

In addition to COMP's Member Contributed symposia, the following organized symposia are planned for the Philadelphia (fall 2012) National ACS Meeting:

Exploring Potential Energy Surfaces in Quantum Chemistry. A Tribute to H. Bernhard Schlegel [Website]

Hrant P. Hratchian (Gaussian, Inc) and Xiaosong Li (University of Washington)

The potential energy surface (PES) provides a central interconnect for the experimentally observed behavior of molecular systems and the theoretical description of that behavior. Indeed, the shape and contour of the PES dictate the structure and dynamics of molecular systems, and most spectroscopies can be studied as a response of the PES to one or more external perturbations. From geometry optimization to ab initio molecular dynamics, the development of efficient PES exploration methods tailored for quantum chemistry have played a crucial role in expanding the applicability and importance of modern computational chemistry in scientific studies.  This symposium honors H. Bernhard Schlegel on the occasion of the 30th anniversary of his landmark “Berny Optimization” paper [J. Comp. Chem., 3, pp214-218 (1982)], and will explore the current state of the field. Discussion topics will include new developments in geometry optimization, ground and excited state dynamics, QM/MM energy surface exploration, and novel applications of such techniques for investigating and understanding chemical questions.

Drug discovery in tyrosine kinase inhibitors and drug resistance

J. Phillip Bowen (Mercer University) & Haizhen Zhong (University of Nebraska – Omaha)

Significant progress has been made in the past three years in small molecule design that target pathways critical in angiogenesis. Aberrant angiogenesis – the formation of new blood vessels from pre-existing blood vessels and vascular endothelial cells – has been observed in many disease states, including inflammation, peptic ulcers, and cancer. In recent years, there are more than 10 tyrosine kinase inhibitors approved by the FDA as anticancer therapeutics, including gefitinib, erlotinib, dasatinib, sunitinib, sorafenib, lapatinib, pazopanib, and etc. There are more than 19 kinase inhibitors targeting EGFR and VEGFR entering clinical trials. VEGFR (vascular endothelial growth factor receptor) and EGFR (endothelial growth factor receptor) are two important enzymes regulating tumor growth and metastasis. Although these VEGFR/EGFR inhibitors are very effective against lung, breast, colorectal, and renal cancer, mutations do evolve. The evolving mutants reduce the sensitivity of cancer cells toward the above therapeutic agents.

This symposium will provide a platform for scientists to discuss approaches to circumvent or overcome mutations observed in VEGFR/EGFR kinase. This forum should provide effective communications in advances in this important research area and will assist scientists in the design of the next generation of efficacious tyrosine kinase inhibitors against resistant strains.

Recent Advances in Studies of Molecular Processes at Liquid Interfaces

Liem X. Dang (Pacific Northwest National Laboratory) & Hongfei Wang (Pacific Northwest National Laboratory)

Reactions that proceed at interfaces are also highly dependent on the interactions between the interfacial solvent and solute molecules. The interfacial structure and properties of molecules at interfaces are generally very different from those in the bulk liquid. Therefore, the chemical and physical properties of heterogeneous systems are dependent on understanding of the fundamental molecular interactions that give rise to interfacial molecular structure. This symposium brings together a group of scientists actively working on the development and/or improvement of techniques that describe the solvation in heterogeneous environments (i.e., liquid/vapor and liquid/liquid interfaces). All of the advances offer new possibilities in addressing a wide range of problems in many disciplines, such as physical science, chemical physics and materials research. The purpose of this symposium is to feature both state-of-the-art theoretical and experimental techniques for understanding chemistry and solvation at liquid interfaces, and to explore new applications of these methods. Possible topics for the symposium include, but are not limited to, reactions at liquid surfaces, ion distribution, spectroscopy, vibration relaxation, and solvation effects. We expect a large attendance at this symposium from scientists and students from several disciplines and this symposium will facilitate fundamental research as well as advanced scientific education. 

Recent advances in Quantum Monte Carlo

Emanuele "Manny" Curotto (Arcadia University)

Simulations of crowding, confinement, and cellular environments

Michael Feig (Michigan State University)

Computational studies of macromolecular systems are often carried out with single molecules at infinite dilution whereas realistic environments are more complex. In particular, biological environments present a significant degree of crowding and confinement due to very high concentrations of nearby biomolecules. While this subject has been studied for some time, there is now renewed interest following new experimental data, increasing computer power, and advances in computational methodology. The goal of the symposium is to discuss recent computational studies in this area covering both biological and non-biological crowded and confined environments. It aims to provide a broad perspective in terms of both physical chemistry and computational methodology.

Scripting and Programming: Drug Discovery and High Performance Computing in the Cloud

Brian Moldover (B-Tech Consulting, Ltd) & Zheng Yang (Boehringer Ingelheim Pharmaceuticals Inc.)

Continuum Solvation Modeling in Biological Systems: Developments and Applications

Ray Luo (University of California, Irvine) & Emil Alexov (Clemson University)

Continuum solvation modeling offers a unique opportunity for more efficient biomolecular simulations without the loss of atomic-level resolution for biomolecules. New methods and new ideas in continuum solvation, coupled with developments in sampling algorithms, classical force fields, and quantum approximations, are proven to be useful for the entire biomedical community in a broad range of studies of biomolecular structures, dynamics, and functions.  Our planned symposium “Continuum Solvation Modeling in Biological Systems: Developments and Applications” offers a platform for developers and other practitioners to exchange ideas to further our community wide efforts in this field. We anticipate that the symposium will cover various aspects of continuum solvation modeling in molecular biology including methodology developments, applications, and computational and theoretical approaches to model the roles of electrostatics in particular reactions in molecular biology.

Multiscale Modeling of Biomolecular Systems

Payel Das (IBM Thomas J. Watson Research Center) & Silvina Matysiak (University of Maryland)

CSAR 2011-2012 Benchmark Exercise

Heather A Carlson (University of Michigan) & James B Dunbar Jr (University of Michigan)

In late 2011, CSAR initiated a blinded exercise to provide members of the docking and scoring community an opportunity to test their methods.  The unpublished data sets were provided by two pharmaceutical companies and colleagues at the University of Michigan, Ann Arbor.  Participants provided both docked poses and affinity predictions.  The exercise closed in the spring of 2012.  Results for that exercise will be presented, and individual groups will discuss the insights gained through their participation.

Characterization and Screening of Databases of Porous Materials

Maciej Haranczyk (Lawrence Berkeley National Laboratory) & Michael W. Deem (Rice University)

Crystalline porous materials are an exciting group of materials with many current and even more envisioned applications. They can be used, for example, as catalysts or as materials for separations and storage of chemical species. This symposium will be focused on tools and approaches that are being developed in order to the search enormous chemical space of these materials and discover the best structures for these applications. 

The list of to-be-discussed topics includes: (a) enumeration and prediction of crystal structures of porous materials; (b) methods and tools for computational characterization of materials; (c) novel structure representations and their applications to materials’ similarity, diversity selection and classification; (d) material databases and search engines; and (e) high-level approaches and case studies combining any or all of (a)-(d).

Understanding and Predicting the Role of Water in drug design

Jean-Francois Truchon (Chemical Computing Group, Inc), Vijay Panda (Stanford University) & Raul Alvarez (Chemical Computing Group, Inc)

Can we improve drug design with better computational treatment of water? Theories and methods will be explored, assessing evidence and validation techniques on the role of structured water in protein:ligand interactions.

Standing Invited Symposium

Perspectives in Applied Computational Methods

Cynthia Bancale (OpenEye Scientific Software, Inc), Carsten Detering (BioSolveIT GmbH) & Raul Alvarez (Chemical Computing Group, Inc)