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The quality of biomolecular simulations critically depends on the accuracy of the force field used to calculate the potential energy of the molecular configurations. Currently, most simulations employ non-polarisable force fields, which…
Multiscale simulations are essential in the biomedical domain to accurately model human physiology. We present a modular approach for designing, constructing and executing multiscale simulations on a wide range of resources, from desktops…
Computational chemistry allows researchers to experiment in sillico: by running a computer simulations of a biological or chemical processes of interest. Molecular dynamics with molecular mechanics model of interactions simulates N-body…
Bionic underwater robots have demonstrated their superiority in many applications. Yet, training their intelligence for a variety of tasks that mimic the behavior of underwater creatures poses a number of challenges in practice, mainly due…
Computational methods are the most effective tools we have besides scientific experiments to explore the properties of complex biological systems. Progress is slowing because digital silicon computers have reached their limits in terms of…
We revise fundamental concepts in the dynamics of open quantum systems in the light of modern developments in the field. Our aim is to present a unified approach to the quantum evolution of open systems that incorporates the concepts and…
Simulating quantum mechanics is known to be a difficult computational problem, especially when dealing with large systems. However, this difficulty may be overcome by using some controllable quantum system to study another less controllable…
Synthetic biology is a recent area of biological engineering, whose aim is to provide cells with novel functionalities. A number of important results regarding the development of control circuits in synthetic biology have been achieved…
The objective of this short report is to reconsider the subject of bioinformatics as just being a tool of experimental biological science. To do that, we introduce three examples to show how bioinformatics could be considered as an…
A new type of quantum simulator is proposed which can simulate any quantum many-body system in an isomorphic manner. It can actually synthesize a duplicate of the system to be simulated. The isomorphic simulation has the great advantage…
A method is presented which allows for a tremendous speed-up of computer simulations of statistical systems by orders of magnitude. This speed-up is achieved by means of a new observable, while the algorithm of the simulation remains…
Quantum computers can in principle solve certain problems exponentially more quickly than their classical counterparts. We have not yet reached the advent of useful quantum computation, but when we do, it will affect nearly all scientific…
The concept of molecular mechanics force field has been widely accepted nowadays for studying various processes in biomolecular systems. In this paper, we suggest a modification for the standard CHARMM force field that permits simulations…
In the dawn of computer science and the eve of neuroscience we participate in rebirth of neuroscience due to new technology that allows us to deeply and precisely explore whole new world that dwells in our brains.
Research in the area of Cyber-Physical Systems (CPS) is hampered by the lack of available project environments in which to explore open challenges and to propose and rigorously evaluate solutions. In this "New Ideas and Emerging Results"…
Machine learning potentials offer a revolutionary, unifying framework for molecular simulations across scales, from quantum chemistry to coarse-grained models. Here, I explore their potential to dramatically improve accuracy and scalability…
Some common systems modelling and simulation approaches for immune problems are Monte Carlo simulations, system dynamics, discrete-event simulation and agent-based simulation. These methods, however, are still not widely adopted in…
Sensors play a fundamental role in achieving the complex behaviors typically found in biological organisms. However, their potential role in the design of artificial agents is often overlooked. This often results in the design of robots…
Ribosomes are critical biomolecular nanomachines responsible for protein synthesis in all known organisms. The function and dynamics of ribosomes can be studied using molecular dynamics computer simulations. Although this task remains…
With increased access to data and the advent of computers, the use of statistical tools and numerical simulations is becoming commonplace for ecologists. These approaches help improve our understanding of ecological phenomena and their…