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Computing long-timescale kinetics of biomolecular processes remains a major challenge for atomistic simulations. A way out is to exploit local kinetic information to construct the global stationary flux across the reaction space. The…
Local interactions among biomolecules, and the role played by their environment, have gained increasing attention in modelling biochemical reactions. By defining the automaton of molecular perceptions, we explore an agent-based…
Topology optimization is computationally demanding that requires the assembly and solution to a finite element problem for each material distribution hypothesis. As a complementary alternative to the traditional physics-based topology…
We consider algorithmic approaches to the D-optimality problem for cases where the input design matrix is large and highly structured, in particular implicitly specified as a full quadratic or linear response-surface model in several levels…
Inspired by decomposition problems in rule-based formalisms in Computational Systems Biology and recent work on compositionality in graph transformation, this paper proposes to use arbitrary colimits to "deconstruct" models of reactions in…
For simulation studies of (macro) molecular liquids it would be of significant interest to be able to adjust or increase the level of resolution within one region of space, while allowing for the free exchange of molecules between open…
In this paper we present a computational modeling account of an active self in artificial agents. In particular we focus on how an agent can be equipped with a sense of control and how it arises in autonomous situated action and, in turn,…
This paper addresses the design of an optimization-based cooperative path-following control law for multiple robotic vehicles that optimally balances the transient trade-off between coordination and path-following errors. To this end, we…
It is an attractive hypothesis that the spatial structure of visual cortical architecture can be explained by the coordinated optimization of multiple visual cortical maps representing orientation preference (OP), ocular dominance (OD),…
High-performance catalysts are crucial for sustainable energy conversion and human health. However, the discovery of catalysts faces challenges due to the absence of efficient approaches to navigating vast and high-dimensional structure and…
Disordered molecular systems such as amorphous catalysts, organic thin films, electrolyte solutions, and water are at the cutting edge of computational exploration today. Traditional simulations of such systems at length-scales relevant to…
While 2D occupancy maps commonly used in mobile robotics enable safe navigation in indoor environments, in order for robots to understand and interact with their environment and its inhabitants representing 3D geometry and semantic…
A scarcity of known chemical kinetic parameters leads to the use of many reaction rate estimates, which are not always sufficiently accurate, in the construction of detailed kinetic models. To reduce the reliance on these estimates and…
Simulation schemes that allow to change molecular representation in a subvolume of the simulation box while preserving the equilibrium with the surrounding introduce conceptual problems of thermodynamic consistency. In this work we present…
Efficient discovery of electrocatalysts for electrochemical energy conversion reactions is of utmost importance to combat climate change. With the example of the oxygen reduction reaction we show that by utilising a data-driven discovery…
We present a new adaptive resolution technique for efficient particle-based multiscale molecular dynamics (MD) simulations. The presented approach is tailor-made for molecular systems where atomistic resolution is required only in spatially…
Despite the modern level of development of computational chemistry methods and techno-logical progress, fast and accurate determination of solvation free energy remains a huge problem for physical chemists. In this paper, we describe two…
Natural, social, and artificial multi-agent systems usually operate in dynamic environments, where the ability to respond to changing circumstances is a crucial feature. An effective collective response requires suitable information…
We present a new optimization-based method for atomistic-to-continuum (AtC) coupling. The main idea is to cast the coupling of the atomistic and continuum models as a constrained optimization problem with virtual Dirichlet controls on the…
Biochemical reactions involving three or more reactants, called higher-molecular reactions, play an important role in theoretical systems and synthetic biology. In particular, such reactions underpin a variety of important bio-dynamical…