8 research outputs found
Exploring the landscapes of "computing": digital, neuromorphic, unconventional -- and beyond
The acceleration race of digital computing technologies seems to be steering
toward impasses -- technological, economical and environmental -- a condition
that has spurred research efforts in alternative, "neuromorphic" (brain-like)
computing technologies. Furthermore, since decades the idea of exploiting
nonlinear physical phenomena "directly" for non-digital computing has been
explored under names like "unconventional computing", "natural computing",
"physical computing", or "in-materio computing". This has been taking place in
niches which are small compared to other sectors of computer science. In this
paper I stake out the grounds of how a general concept of "computing" can be
developed which comprises digital, neuromorphic, unconventional and possible
future "computing" paradigms. The main contribution of this paper is a
wide-scope survey of existing formal conceptualizations of "computing". The
survey inspects approaches rooted in three different kinds of background
mathematics: discrete-symbolic formalisms, probabilistic modeling, and
dynamical-systems oriented views. It turns out that different choices of
background mathematics lead to decisively different understandings of what
"computing" is. Across all of this diversity, a unifying coordinate system for
theorizing about "computing" can be distilled. Within these coordinates I
locate anchor points for a foundational formal theory of a future
computing-engineering discipline that includes, but will reach beyond, digital
and neuromorphic computing.Comment: An extended and carefully revised version of this manuscript has now
(March 2021) been published as "Toward a generalized theory comprising
digital, neuromorphic, and unconventional computing" in the new open-access
journal Neuromorphic Computing and Engineerin
Structural decomposition and structural relaxation of solvation shells of hydrated molecular ionic liquids and protein solutions
Die vorliegende Arbeit liefert neue methodische Beitraege zur Untersuchung der
Struktur und Dynamik von Biomolekuelen in Loesung mittels Voronoi-Analyse von Computersimulationen.
Dabei werden sowohl kollektive wie auch Einteilchen-Eigenschaften der Solvathuellen und des Bulk-Mediums
betrachtet.
Als Modellproteine dienen Ubiquitin (PDB-code: 1UBQ), Calbindin (1CLB) und eine Phospholipase (2PLD)
deren Solvatation in Wasser einen wesentlichen Bestandteil dieser Arbeit darstellt. Darueber hinaus werden Vorstudien
zu Molekularen Ionischen Fluessigkeiten (MIL) angestellt die in den letzten Jahren unter anderem als umweltvertraegliche
polare Loesungsmittel in den Vordergrund getreten sind. Trifluoroazetat-, Tetrafluoroborat-
und Trifluoromethylsulfonat- Salze von alkyliertem Imidazolium werden einerseits in Reinform, andererseits in Mischung mit
Wasser untersucht.
Neu an dieser Arbeit ist zunaechst die Atom-aufgeloeste Tesselierung, die fuer Systeme mit 30000 Atomen
mit periodischen Randbedingungen ueber hundertausende Zeitschritte sehr rechenintensiv, und daher
nur durch die effiziente Implementierung geeigneter Algorithmen zu bewerkstelligen ist.
Auf dieser Grundlage werden weitestgehend parameterfreie Ansaetze zur lokalen und globalen Strukturanalyse entwickelt
die einerseits mit konventionellen Methoden wie etwa Radialen Verteilungsfunktionen und Orientierungskorrelationsfunktionen
verglichen werden, andererseits zusaetzliche Moeglichkeiten der Interpretation bieten.
Position und Orientierung von benachbarten Molekuelen kann direkt anhand von graphentheoretischen Interaktionen beschrieben
und interpretiert werden. Ein Markov-Modell fuer die Dynamik innerhalb und zwischen einzelnen Solvathuellen wird entwickelt
und auf MIL Systeme angewendet.The present work provides new methodical contributions to investigation of structural and dynamic behaviour of solvated biomolecules
using Voronoi analysis of computer simulations. Thereby, collective as well as single particle properties of solvation shells
and the bulk medium are considered.
The three proteins ubiquitin (PDB-code: 1UBQ), calbindin (1CLB) and phospholipase (2PLD) serve as model systems. The study of their
solvation in water is an integral part of this work. Moreover, preliminary studies of Molecular Ionic Liquids (MIL) are being
made, that have come to the fore in recent years as environmentally compliant polar solvents. Alkylated imidazolium salts of
Trifluoroacetate, Tetrafluoroborate and Trifluoromethylsulfonate are analysed in the pure form as well as mixed with water.
For one thing, new in this work is the atom-resolved tesselation, that is computationally demanding for systems with about 30000 atoms
and periodic boundary conditions over 100-thousands of time steps and hence is to be managed only by the efficient implementation
of suitable algorithms.
Widely parameter free approaches to local and global structure analysis are developed on this basis and compared
to conventional methods like radial distribution functions and orientation correlation functions. Furthermore,
they provide additional possibilities for interpretation.
Position and orientation of neighbouring molecules can be described and interpreted directly by graph theoretical interactions.
A Markov model for dynamics within and between solvation shells is being developed and applied to MIL systems