28 papers · ranked by Valyu relevance
Kate Harline, Jesús Martínez-Gómez, Chelsea D. Specht, Adrienne H. K. Roeder
'Adrienne H. K. Roeder'] Modeling has become a popular tool for inquiry and discovery across biological disciplines. Models allow biologists to probe complex questions and to guide experimentation. Modeling literacy among biologists, however, has not always kept pace with the rise in popularity of these techniques and…
Hugo Geerts, James E. Barrett
With the success rate of drugs for CNS indications at an all-time low, new approaches are needed to turn the tide of failed clinical trials. This paper reviews the history of CNS drug Discovery over the last 60 years and proposes a new paradigm based on the lessons learned. The initial wave of successful therapeutics…
Beatrix C. Hiesmayr, Marc‐Thorsten Hütt
A recent trend in mathematical modeling is to publish the computer code together with the research findings. Here we explore the formal question, whether and in which sense a computer implementation is distinct from the mathematical model. We argue that, despite the convenience of implemented models, a set of implicit…
Andreas Tolk, Saikou Y. Diallo, José J. Padilla, Ross Gore
Epistemology is the branch of philosophy that deals with gaining knowledge. It is closely related to ontology. The branch that deals with questions like "What is real?" and "What do we know?" as it provides these components. When using modeling and simulation, we usually imply that we are doing so to either apply…
Jacek A Kopec, Philippe Finès, Douglas G Manuel, David L Buckeridge + 9 more
Background Computer simulation models are used increasingly to support public health research and policy, but questions about their quality persist. The purpose of this article is to review the principles and methods for validation of population-based disease simulation models. Methods We developed a comprehensive…
Elise Laruelle, Katia Belcram, Alain Trubuil, Jean-Christophe Palauqui + 1 more
Noise plays a major role in cellular processes and in the development of tissues and organs. Several studies have examined the origin, the integration or the accommodation of noise in gene expression, cell growth and elaboration of organ shape. By contrast, much less is known about variability in cell division plane…
Juan J. Pérez, Ana González-Suárez, Enrique Nadal, Enrique Berjano
The state of the art in computer modeling of radiofrequency catheter ablation (RFCA) only considers a static model, i.e. it does not allow modeling ablation electrode displacements induced by tissue movement due to heartbeats. This feature is theoretically required, since heartbeat-induced changes in contact force can…
Nestor V. Torres, Guido Santos
In this communication, we introduce a general framework and discussion on the role of models and the modeling process in the field of biosciences. The objective is to sum up the common procedures during the formalization and analysis of a biological problem from the perspective of Systems Biology, which approaches the…
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'…
Hadass R. Jessel, Lior Aharoni, Sol Efroni, Ido Bachelet
Natural biological structures are often complex and cannot be mapped directly to genes, being therefore impossible to explore by traditional biological tools. In contrast, digitizing these structures enables to explore their properties and behavior under specific conditions, by means of computational manipulations…
N. Furian, M. O’Sullivan, C. Walker, S. Vössner + 1 more
Conceptual Modeling (CM) is a fundamental step in a simulation project. Nevertheless, it is only recently that structured approaches towards the definition and formulation of conceptual models have gained importance in the Discrete Event Simulation (DES) community. As a consequence, frameworks and guidelines for…
Konrad Hinsen
Computational techniques have revolutionized many aspects of scientific research over the last few decades. Experimentalists use computation for data analysis, processing ever bigger data sets. Theoreticians compute predictions from ever more complex models. However, traditional articles do not permit the publication…
Szymon Wasik, Tomasz Prejzendanc, Jacek Blazewicz
Computational modeling is an important element of systems biology. One of its important applications is modeling complex, dynamical, and biological systems, including viral infections. This type of modeling usually requires close cooperation between biologists and mathematicians. However, such cooperation often faces…
Adelinde M. Uhrmacher, Peter I. Frazier, Reiner Hähnle, Franziska Klügl + 8 more
'Franziska Klügl' 'Fabian Lorig' 'Bertram Ludäscher' 'Laura Nenzi' 'Cristina Ruiz-Martín' 'Bernhard Rumpe⋆' 'Claudia Szabo' 'Gabriel Wainer' 'Pia Wilsdorf'] Simulation has become, in many application areas, a sine-qua-non. Most recently, COVID-19 has underlined the importance of simulation studies and limitations in…
Juan M. Durán
The book is organized as follows. In chapter 1, I address the question 'what are computer simulations?' by giving an historical overview of the concept. Tracking back the concept of computer simulation to the early 1960s, we will soon realize that many contemporary definitions owe much to these early attempts. A proper…
Lesley A. Ogilvie, Aleksandra Kovachev, Christoph Wierling, Bodo M. H. Lange + 1 more
'Bodo M. H. Lange' 'Hans Lehrach'] Every patient and every disease is different. Each patient therefore requires a personalized treatment approach. For technical reasons, a personalized approach is feasible for treatment strategies such as surgery, but not for drug-based therapy or drug development. The development of…
Barak Raveh, Liping Sun, Kate L. White, Tanmoy Sanyal + 11 more
Comprehensive modeling of a whole cell requires an integration of vast amounts of information on various aspects of the cell and its parts. To divide-and-conquer this task, we introduce Bayesian metamodeling, a general approach to modeling complex systems by integrating a collection of heterogeneous input models. Each…
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…
Anna Matuszyńska, Oliver Ebenhöh, Matias D. Zurbriggen, Daniel C. Ducat + 1 more
Synthetic biology designs and constructs new biological parts, devices and systems with predetermined functionalities. With the unlimited ability to synthesise any DNA and RNA and transfer it to almost any organism, we are at the dawn of a new era in which biology is being recreated in ways never before possible. It…
Wei Zhang, Jonathan A Fine, Christopher Sculley, Jordon McGraw + 1 more
The representation of complex biomolecular structures and interactions is a difficult challenge across life sciences. Researchers and students use unintuitive 2D representations to gain an intuitive understanding of 3D space and molecular interactions. Since this is cumbersome for complex structures, such as…
Niloofar Shahidi, Michael Pan, Soroush Safaei, Kenneth Tran + 2 more
Simulating complex biological and physiological systems and predicting their behaviours under different conditions remains challenging. Breaking systems into smaller and more manageable modules can address this challenge, assisting both model development and simulation. Nevertheless, existing computational models in…
Christopher Schölzel, Valeria Blesius, Gernot Ernst, Andreas Dominik
Reproducible, understandable models that can be reused and combined to true multi-scale systems are required to solve the present and future challenges of systems biology. However, many mathematical models are still built for a single purpose and reusing them in a different context can be challenging due to an…
Stefan Ivanov
In order for computer-aided drug design to fulfil its long held promise of delivering new medicines faster and cheaper, extensive development and validation work must be done first. This pertains particularly to molecular dynamics force fields where one important aspect – the hydration free energy (HFE) of small…
Mark Burgin, Gordana Dodig-Crnković
We need much better understanding of information processing and computation as its primary form. Future progress of new computational devices capable of dealing with problems of big data, internet of things, semantic web, cognitive robotics and neuroinformatics depends on the adequate models of computation. In this…
Daiki Erikawa, Nobuaki Yasuo, Masakazu Sekijima
Automatic optimization methods for compounds in the vast compound space are important for drug discovery and material design. Several machine learning-based molecular generative models for drug discovery have been proposed, but most of these methods generate compounds from scratch and are not suitable for exploring and…
Authors not listed
The rapid advancements in computational methods have revolutionized drug discovery and development. These methods, ranging from molecular modelling to machine learning algorithms, have drastically increased in number and sophistication. However, a comprehensive understanding of these diverse approaches is essential for…
Samuel Gill, Nathan M. Lim, Patrick Grinaway, Ariën S. Rustenburg + 4 more
Accurately predicting protein-ligand binding is a major goal in computational chemistry, but even the prediction of ligand binding modes in proteins poses major challenges. Here, we focus on solving the binding mode prediction problem for rigid fragments. That is, we focus on computing the dominant placement…
Authors not listed
Step-by-step thinking is essential in all domains of chemical sciences and engineering. While machine learning tools are broadly used, algorithms that automate reasoning are far less common. We elaborate on seven categories of human reasoning activities and connect each to applications in chemical science and…