26 papers · ranked by Valyu relevance
Oliver Lee, Malte Gather, Eli Zysman-Colman
We describe a new tool for the efficient management of computational chemistry. Digichem is a program that automates and simplifies nearly the entire computational pipeline, including large-scale batch submission of calculations, analysis and results parsing, the generation of 3D density plots and 2D graphs of…
Ban Chen, Shuangshuang Liu, Huiyin Xia, Xican Li + 2 more
'Alan Talevi'] Chinese materia medica (CMM) refers to the medicinal substances used in traditional Chinese medicine. In recent years, CMM has become globally prevalent, and scientific research on CMM has increasingly garnered attention. Computer-aided drug design (CADD) has been employed in Western medicine research…
Milan Toma, Riccardo Concu
All living things are related to one another. Hence, the science of biology is comprehensive in scope. Biology, i.e., studying the structure, function, growth, origin, evolution, and distribution of living organisms is a vast and eclectic field. The science of biology is divided into different branches. Some divisions…
Authors not listed
For decades, computational theoretical chemistry has provided critical insights into molecular behavior, often anticipating experimental discoveries. This review surveys twenty notable examples from the past fifteen years in which computational chemistry successfully predicted molecular structures, reaction mechanisms…
Arthur D Lander
Biological systems are so complex that we must ask: "What purpose does all this complexity serve?" Lander argues that computational biology may help provide answers
Tülin Kaman, Rouben Rostamian, Shannon Dingman
We introduce a newly designed undergraduate-level interdisciplinary course in scientific computing that aims to prepare students as the next generation of researchoriented computational scientists and engineers. The course offers students opportunities to explore a diverse set of projects and develop the necessary…
Ambrish Kumar Srivastava, Konda Reddy Karnati, Kshatresh Dutta Dubey
Computational methods have become powerful enough to describe the biomolecular structures and their interactions. A variety of methods have been developed and implemented successfully to study biomolecular systems and processes up to a certain level of accuracy. For instance, biomolecular processes are mediated by…
Marcos D. Caballero, M. Hjorth‐Jensen
In this contribution we discuss how to develop a physics curriculum for undergraduate students that includes computing as a central element. Our contribution starts with a definition of computing and pertinent learning outcomes and assessment studies and programs. We end with a discussion on how to implement computing…
J Kyle Medley, Kiri Choi, Matthias König, Lucian Smith + 4 more
The considerable difficulty encountered in reproducing the results of published dynamical models limits validation, exploration and reuse of this increasingly large biomedical research resource. To address this problem, we have developed Tellurium Notebook, a software system that facilitates building reproducible…
Małgorzta Borówko
Rapid advances are taking place in the application of molecular simulations to study complex systems. Molecular simulations are widely used in physics, chemistry, biology, material science, engineering, and even medicine. Each study conducted in a purely theoretical manner can be treated as a simulation. The behavior…
Pablo García‐Risueño, Pablo Ibáñez
The increase of existing computational capabilities has made simulation emerge as a third discipline of Science, lying midway between experimental and purely theoretical branches [1, 2]. Simulation enables the evaluation of quantities which otherwise would not be accessible, helps to improve experiments and provides…
Matthias König
To address the issue of reproducibility in computational modeling we developed the concept of an executable simulation model (EXSIMO). An EXSIMO combines model, data and code with the execution environment to run the computational analysis in an automated manner using tools from software engineering. Key components are…
Siddharth Sinha, Benjamin Tam, San Ming Wang, Hugo A. L. Filipe
Molecular Dynamics (MD) Simulations is increasingly used as a powerful tool to study protein structure-related questions. Starting from the early simulation study on the photoisomerization in rhodopsin in 1976, MD Simulations has been used to study protein function, protein stability, protein-protein interaction…
Alan Aspuru-Guzik, Roland Lindh, Markus Reiher
To date, the program for the development of methods and models for atomistic and continuum simulation directed toward chemicals and materials has reached an incredible degree of sophistication and maturity. Currently, one can witness an increasingly rapid emergence of advances in computing, artificial intelligence, and…
Samantha Durdy, Cameron J. Hargreaves, Mark Dennison, Benjamin Wagg + 5 more
The discovery of new materials often requires collaboration between experimental and computational chemists. Web based platforms allow more flexibility in this collaboration by giving access to computational tools without the need for access to computational researchers. We present Liverpool Materials Discovery Server…
Marcos D. Caballero, Steven J. Pollock
Much of the research done by modern physicists would be impossible without the use of computation. And yet, while computation is a crucial tool of practicing physicists, physics curricula do not generally reflect its importance and utility. To more tightly connect undergraduate preparation with professional practice…
Samarth Sandeep, Sona Aramyan, Armen H. Poghosyan, Vaibhav Gupta
Determining an optimal protein configuration for the employment of protein binding analysis as completed by Temperature based Replica Exchange Molecular Dynamics (T-REMD) is an important process in the accurate depiction of a protein’s behavior in different solvent environments, especially when determining a protein’s…
Tan-Nhu Nguyen, Marie-Christine Ho Ba Tho, Tien-Tuan Dao
Simulating deformations of soft tissues is a complex engineering task, and it is even more difficult when facing the constraint between computation speed and system accuracy. However, literature lacks of a holistic review of all necessary aspects (computational approaches, interaction devices, system architectures, and…
David S. Cerutti, Rafal Wiewiora, Simon Boothroyd, Woody Sherman
The Structure and TOpology Replica Molecular Mechanics (STORMM) code is a next-generation molecular simulation engine and associated libraries optimized for performance on fast, multicore central processor units (CPUs) and graphics processing units (GPUs) with independent memory and tens of thousands of threads. STORMM…
Mahyuddin K. M. Nasution, Rahmat Hidayat, Rahmad Syah
— Possible for science itself, conceptually, to have and will understand differently, let alone science also seen as technology, such as computer science. After all, science and technology are viewpoints diverse by either individual, community, or social. Generally, it depends on socioeconomic capabilities. So it is…
Ulrich Rüde, Karen Willcox, Lois Curfman McInnes, Hans De Sterck + 29 more
'George Biros' 'Hans Bungartz' 'James Corones' 'Evin Cramer' 'James L. Crowley' 'Omar Ghattas' 'Max Gunzburger' 'Michael Hanke' 'Robert Harrison' 'Michael A. Heroux' 'Jan S. Hesthaven' 'Peter K. Jimack' 'Chris R. Johnson' 'Kirk E. Jordan' 'David E. Keyes' 'Rolf Krause' 'Vipin Kumar' 'Stefan Mayer' 'Juan M López Meza'…
Aasakiran Madamanchi, Madison Thomas, Alejandra Magana, Randy Heiland + 1 more
There is growing awareness of the need for mathematics and computing to quantitatively understand the complex dynamics and feedbacks in the life sciences. Although several institutions and research groups are conducting pioneering multidisciplinary research, communication and education across fields remains a…
Andrew McCluskey, Miguel Rivera, Antonia Mey
The role of computing in the chemical sciences is changing. Previously the domain of the theoretical or computational chemist, advanced digital skills, including data analysis and simulation, are becoming extremely relevant to all. Here, we discuss the importance of integrating computing and digital skills into an…
Hang Phuong Nguyen, Hyun-Joo Lee, Sungmin Kim
Purpose In this study, we proposed establishing an automatic computer-assisted surgical planning approach based on average population models. Methods We built the average population models from humerus datasets using the Advanced Normalization Toolkits (ANTs) and Shapeworks. Experiments include (1) evaluation of the…
Till Köster, Philipp Henning, Tom Warnke, Adelinde Uhrmacher
Compartmentalization is vital for cell biological processes. The field of rule-based stochastic simulation has acknowledged this, and many tools and methods have capabilities for compartmentalization. However, mostly, this is limited to a static compartmental hierarchy and does not integrate compartmental changes.…
Neil Thompson, Shuning Ge, Gabriel F. Manso
Denizens of Silicon Valley have called Moore's Law "the most important graph in human history," and economists have found that Moore's Law-powered I.T. revolution has been one of the most important sources of national productivity growth. But data substantiating these claims tend to either be abstracted — for example…