Toward transferable interatomic van der Waals interactions without electrons: The role of multipole electrostatics and many-body dispersion

We estimate polarizabilities of atoms in molecules without electron density, using a Voronoi tesselation approach instead of conventional density partitioning schemes. The resulting atomic dispersion coefficients are calculated, as well as many-body dispersion effects on intermolecular potential energies. We also estimate contributions from multipole electrostatics and compare them to dispersion. We assess the performance of the resulting intermolecular interaction model from dispersion and electrostatics for more than 1,300 neutral and charged, small organic molecular dimers. Applications to water clusters, the benzene crystal, the anti-cancer drug ellipticine---intercalated between two Watson-Crick DNA base pairs, as well as six macro-molecular host-guest complexes highlight the potential of this method and help to identify points of future improvement. The mean absolute error made by the combination of static electrostatics with many-body dispersion reduces at larger distances, while it plateaus for two-body dispersion, in conflict with the common assumption that the simple $1/R^6$ correction will yield proper dissociative tails. Overall, the method achieves an accuracy well within conventional molecular force fields while exhibiting a simple parametrization protocol.Comment: 13 pages, 8 figure

Exploiting replication in distributed systems

Techniques are examined for replicating data and execution in directly distributed systems: systems in which multiple processes interact directly with one another while continuously respecting constraints on their joint behavior. Directly distributed systems are often required to solve difficult problems, ranging from management of replicated data to dynamic reconfiguration in response to failures. It is shown that these problems reduce to more primitive, order-based consistency problems, which can be solved using primitives such as the reliable broadcast protocols. Moreover, given a system that implements reliable broadcast primitives, a flexible set of high-level tools can be provided for building a wide variety of directly distributed application programs

A reduced semantics for deciding trace equivalence using constraint systems

Many privacy-type properties of security protocols can be modelled using trace equivalence properties in suitable process algebras. It has been shown that such properties can be decided for interesting classes of finite processes (i.e., without replication) by means of symbolic execution and constraint solving. However, this does not suffice to obtain practical tools. Current prototypes suffer from a classical combinatorial explosion problem caused by the exploration of many interleavings in the behaviour of processes. M\"odersheim et al. have tackled this problem for reachability properties using partial order reduction techniques. We revisit their work, generalize it and adapt it for equivalence checking. We obtain an optimization in the form of a reduced symbolic semantics that eliminates redundant interleavings on the fly.Comment: Accepted for publication at POST'1

Composing Interfering Abstract Protocols

The undisciplined use of shared mutable state can be a source of program errors when aliases unsafely interfere with each other. While protocol-based techniques to reason about interference abound, they do not address two practical concerns: the decidability of protocol composition and its integration with protocol abstraction. We show that our composition procedure is decidable and that it ensures safe interference even when composing abstract protocols. To evaluate the expressiveness of our protocol framework for safe shared memory interference, we show how this same protocol framework can be used to model safe, typeful message-passing concurrency idioms

Self-Consistent Assignment of Asparagine and Glutamine Amide Rotamers in Protein Crystal Structures

SummaryThe current protein structure database contains unfavorable Asn/Gln amide rotamers in the order of 20%. Here, we derive a set of self-consistent potential functions to identify and correct unfavorable rotamers. Potentials of mean force for all heavy atoms are compiled from a database of high-resolution protein crystal structures. Starting from erroneous data, a refinement-correction cycle quickly converges to a self-consistent set of potentials. The refinement is entirely driven by the deposited structure data and does not involve any assumptions on molecular interactions or any artificial constraints. The refined potentials obtained in this way identify unfavorable rotamers with high confidence. Since the state of Asn/Gln rotamers is largely determined by hydrogen bond interactions, the features of the respective potentials are of interest in terms of molecular interactions, protein structure refinement, and prediction. The Asn/Gln rotamer assignment is available as a public web service intended to support protein structure refinement and modeling

DAG-Based Attack and Defense Modeling: Don't Miss the Forest for the Attack Trees

This paper presents the current state of the art on attack and defense modeling approaches that are based on directed acyclic graphs (DAGs). DAGs allow for a hierarchical decomposition of complex scenarios into simple, easily understandable and quantifiable actions. Methods based on threat trees and Bayesian networks are two well-known approaches to security modeling. However there exist more than 30 DAG-based methodologies, each having different features and goals. The objective of this survey is to present a complete overview of graphical attack and defense modeling techniques based on DAGs. This consists of summarizing the existing methodologies, comparing their features and proposing a taxonomy of the described formalisms. This article also supports the selection of an adequate modeling technique depending on user requirements

A Reduced Semantics for Deciding Trace Equivalence

Many privacy-type properties of security protocols can be modelled using trace equivalence properties in suitable process algebras. It has been shown that such properties can be decided for interesting classes of finite processes (i.e., without replication) by means of symbolic execution and constraint solving. However, this does not suffice to obtain practical tools. Current prototypes suffer from a classical combinatorial explosion problem caused by the exploration of many interleavings in the behaviour of processes. M\"odersheim et al. have tackled this problem for reachability properties using partial order reduction techniques. We revisit their work, generalize it and adapt it for equivalence checking. We obtain an optimisation in the form of a reduced symbolic semantics that eliminates redundant interleavings on the fly. The obtained partial order reduction technique has been integrated in a tool called APTE. We conducted complete benchmarks showing dramatic improvements.Comment: Accepted for publication in LMC