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We introduce a logic for knowledge representation and reasoning on protein-protein interactions. Modulo a theory, formulas describe protein structures and dynamic changes. They can be composed in order to add or remove static and dynamic…
Accurately modelling cold and ultracold reactive collisions occuring over deep potential wells, such as \ce{D+ + H2 -> H+ + HD}, requires the development of new theoretical and computational methodologies. One potentially useful framework…
We propose a new and general formalism for elementary chemical reactions where quantum electronic variables are used as reaction coordinates. This formalism is in principle applicable to all kinds of chemical reactions ionic or covalent.…
This paper proposes a new approach to defining and expressing algorithms: the notion of {\it task logical} algorithms. This notion allows the user to define an algorithm for a task $T$ as a set of agents who can collectively perform $T$.…
Modeling processes are the activities of capturing and representing processes and control of their dynamic behavior. Desired features of the model include capture of relevant aspects of a real phenomenon, understandability, and completeness…
The presence of solvent tunes many properties of a molecule, such as its ground and excited state geometry, dipole moment, excitation energy, and absorption spectrum. Because the energy of the system will vary depending on the solvent…
Deep generative models are able to suggest new organic molecules by generating strings, trees, and graphs representing their structure. While such models allow one to generate molecules with desirable properties, they give no guarantees…
In a previous work the authors described a fast high-fidelity computer model for acoustic scattering from multi-layered elastic spheres. This work is now extended with a scaling strategy significantly mitigating the problem of overflow and…
Mathematical methods provide useful framework for the analysis and design of complex systems. In newer contexts such as biology, however, there is a need to both adapt existing methods as well as to develop new ones. Using a combination of…
Dielectric properties of material mixtures are of importance in diagnostics, characterization and design of systems in various engineering fields. In this Letter, we propose a peculiar dielectric mixture expression, which is based on the…
Automatic synthesis from a given specification automatically constructs correct implementation. This frees the user from the mundane implementation work, but still requires the specification. But is specifying easier than implementing? In…
This review discusses research developments and applications of isotachophoresis (ITP) to the initiation, control, and acceleration of chemical reactions, emphasizing reactions involving biomolecular reactants such as nucleic acids,…
Recent developments of the Cascade-Exciton Model (CEM) of nuclear reactions are described. The improved cascade-exciton model as implemented in the code CEM97 differs from the CEM95 version by incorporating new approximations for the…
We examine the problem of generating definite noun phrases that are appropriate referring expressions; i.e, noun phrases that (1) successfully identify the intended referent to the hearer whilst (2) not conveying to her any false…
Recent years have seen an increasing need of high-level specification languages and tools generating code from specifications. In this paper, we introduce a specification language, {\splname}, which is tailored to the writing of syntactic…
Word embeddings are substantially successful in capturing semantic relations among words. However, these lexical semantics are difficult to be interpreted. Definition modeling provides a more intuitive way to evaluate embeddings by…
Understanding mechanisms of rare but important events in complex molecular systems, such as protein folding or ligand (un)binding, requires accurately mapping transition paths from an initial to a final state. The committor is the ideal…
Reaction-diffusion processes are the foundational model for a diverse range of complex systems, ranging from biochemical reactions to social agent-based phenomena. The underlying dynamics of these systems occur at the individual…
The ability to reason beyond established knowledge allows Organic Chemists to solve synthetic problems and to invent novel transformations. Here, we propose a model which mimics chemical reasoning and formalises reaction prediction as…
In this paper, we introduce a novel rule for synthesis of reactive systems, applicable to systems made of n components which have each their own objectives. It is based on the notion of admissible strategies. We compare our novel rule with…