Related papers: The BioDynaMo Project: a platform for computer sim…
Machine learning (ML) has emerged as a pervasive tool in science, engineering, and beyond. Its success has also led to several synergies with molecular dynamics (MD) simulations, which we use to identify and characterize the major…
Computer simulations that demonstrate the valueof novel approaches are crucial to developing more flexibleand robust power systems operations with high penetrations ofrenewable energy at multiple geographic and temporal scales.However,…
We use molecular dynamic to simulate the directional growth of binary mixtures. our results compare very well with analitical and experimental results. This opens up the possibility to probe growth situations which are difficult to reach…
Coupling a quantum many-body system to an external environment dramatically changes its dynamics and offers novel possibilities not found in closed systems. Of special interest are the properties of the steady state of such open quantum…
This article proposes a universal simulation platform for simulating systems undergoing duress. In other words, this paper introduces a total simulation package which includes a number of methods of simulating the flexibility of a given…
Physics students now have access to interactive molecular dynamics simulations that can model and animate the motions of hundreds of particles, such as noble gas atoms, that attract each other weakly at short distances but repel strongly…
Process simulation is gaining attention for its ability to assess potential performance improvements and risks associated with business process changes. The existing literature presents various techniques, generally grounded in process…
Simflowny is an open platform which automatically generates parallel code of scientific dynamical models for different simulation frameworks. Here we present major upgrades on this software to support an extended set of families of models,…
This letter illustrates the opinion of the molecular dynamics (MD) community on the need to adopt a new FAIR paradigm for the use of molecular simulations. It highlights the necessity of a collaborative effort to create, establish, and…
Many real-world dynamic systems, both natural and artificial, are understood to be performing computations. For artificial dynamic systems, explicitly designed to perform computation - such as digital computers - by construction, we can…
Advances in molecular technologies underlie an enormous growth in the size of data sets pertaining to biology and biomedicine. These advances parallel those in the deep learning subfield of machine learning. Components in the differentiable…
So far proposed quantum computers use fragile and environmentally sensitive natural quantum systems. Here we explore the new notion that synthetic quantum systems suitable for quantum computation may be fabricated from smart nanostructures…
Scientific applications produce a huge amount of data, which imposes serious management and analysis challenges. In particular, limitations in current database management systems prevent their adoption in simulation applications, in which…
Recent advances in both theory and computational power have created opportunities to simulate biomolecular processes more efficiently using adaptive ensemble simulations. Ensemble simulations are now widely used to compute a number of…
We describe software and a language for quasibiological computations. Its theoretical basis is a unified theory of complex (adaptive) systems where all laws are regularities of relations between things or agents, and dynamics is made from…
There are many problems in biochemistry that are difficult to study experimentally. Simulation methods are appealing due to direct availability of atomic coordinates as a function of time. However, direct molecular simulations are…
As metabolomics datasets are becoming larger and more complex, there is an increasing need for model-based data integration and analysis to optimally leverage these data. Dynamical models of metabolism allow for the integration of…
This paper describes a simulator of ultrasound-guided prostate biopsies for cancer diagnosis. When performing biopsy series, the clinician has to move the ultrasound probe and to mentally integrate the real-time bi-dimensional images into a…
Monte Carlo simulation is an essential component of experimental particle physics in all the phases of its life-cycle: the investigation of the physics reach of detector concepts, the design of facilities and detectors, the development and…
A model for artificial evolution in native x86 Windows systems has been developed at the end of 2010. In this text, further improvements and additional analogies to natural microbiologic processes are presented. Several experiments indicate…