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A Lagrangian heuristic for satellite range scheduling with resource constraints

Fabrizio Marinelli, Salvatore Nocella, Fabrizio Rossi, Stefano Smriglio
2011 Computers & Operations Research  
The task of scheduling communications between satellites and ground control stations is getting more and more critical since an increasing number of satellites must be controlled by a small set of stations. In such a congested scenario, the current practice, in which experts build hand-made schedules, often leaves a large number of communication requests unserved. We report on our experience in the design of an optimization-based support tool at the European Space Agency. We propose a tight
more » ... -indexed formulation of the problem able to include several complex technological constraints. A non-standard Lagrangian heuristic is then devised which provides near-optimal solutions of a set of largescale test problems arising in the forthcoming GALILEO constellation. The heuristic shows numerical stability and robustness adequate for practical implementation. The resulting tool is used by the Italian reference operator for GALILEO system management and is currently under testing at the European Space Agency.
doi:10.1016/j.cor.2011.01.016 fatcat:7zra4w4k7feyzl5phhfgz2onpi

On LP relaxations for the pattern minimization problem

Alessandro Aloisio, Claudio Arbib, Fabrizio Marinelli
2010 Networks  
We discuss two formulations of the Pattern Minimization Problem: (1) introduced by Vanderbeck, and (2) obtained adding setup variables to the cutting stock formulation by Gilmore-Gomory. Let z LP i (u) be the bound given by the linear relaxation of (i) under a given vector u = (u k ) of parameters. We show that z LP 2 (u) ≥ z LP 1 (u) and provide a class of instances for which the inequality holds strict. We observe that the linear relaxation of both formulations can be solved by the same
more » ... generation procedure, and discuss the critical role of parameters u. The paper is completed by a numerical test comparing the lower bounds obtained through (1) and (2) for different values of u.
doi:10.1002/net.20422 fatcat:75akbg5lvndg3nbyixbuimmk4m

Mathematical programming based debugging

Leo Liberti, Stéphane Le Roux, Jeremy Leconte, Fabrizio Marinelli
2010 Electronic Notes in Discrete Mathematics  
Verifying that a piece of software has no bugs means proving that it has certain desired properties, such as an array index not taking values outside certain bounds. Abstract interpretation is used in the static analysis of code to establish the inclusion-wise smallest set of values (numerical invariant) that the program variables can attain during program execution. Such sets can be used to detect run-time errors without actually running the program. We present a mathematical program that
more » ... mines guaranteed smallest interval invariants of computer programs with integer affine arithmetics and compare our results to existing techniques.
doi:10.1016/j.endm.2010.05.166 fatcat:nerpecbjyzgpzg7k2aragu5koy

Structural Interpretation of Hydrogen-Deuterium Exchange with Maximum-Entropy Simulation Reweighting [article]

Richard T Bradshaw, Fabrizio Marinelli, José D Faraldo-Gómez, Lucy R Forrest
2019 bioRxiv   pre-print
Our approach is related to that of Marinelli & Fiorin (46) , in which the only bias applied is that strictly required to conform to the experiments, following the so-called maximum-entropy principle  ... 
doi:10.1101/769398 fatcat:3d2jcr7avfdkrbxydeznbexiie

Mathematical programming: Turing completeness and applications to software analysis

Leo Liberti, Fabrizio Marinelli
2014 Journal of combinatorial optimization  
Mathematical Programming is Turing complete, and can be used as a general-purpose declarative language. We present a new constructive proof of this fact, and showcase its usefulness by discussing an application to finding the hardest input of any given program running on a Minsky Register Machine. We also discuss an application of Mathematical Programming to software verification obtained by relaxing one of the properties of Turing complete languages.
doi:10.1007/s10878-014-9715-3 fatcat:kro37jxfmrdadbd7yn5qez3r7u

Ensemble-Biased Metadynamics: A Molecular Simulation Method to Sample Experimental Distributions

Fabrizio Marinelli, José D. Faraldo-Gómez
2015 Biophysical Journal  
We introduce an enhanced-sampling method for molecular dynamics (MD) simulations referred to as ensemblebiased metadynamics (EBMetaD). The method biases a conventional MD simulation to sample a molecular ensemble that is consistent with one or more probability distributions known a priori, e.g., experimental intramolecular distance distributions obtained by double electron-electron resonance or other spectroscopic techniques. To this end, EBMetaD adds an adaptive biasing potential throughout
more » ... simulation that discourages sampling of configurations inconsistent with the target probability distributions. The bias introduced is the minimum necessary to fulfill the target distributions, i.e., EBMetaD satisfies the maximum-entropy principle. Unlike other methods, EBMetaD does not require multiple simulation replicas or the introduction of Lagrange multipliers, and is therefore computationally efficient and straightforward in practice. We demonstrate the performance and accuracy of the method for a model system as well as for spin-labeled T4 lysozyme in explicit water, and show how EBMetaD reproduces three double electron-electron resonance distance distributions concurrently within a few tens of nanoseconds of simulation time. EBMetaD is integrated in the open-source PLUMED plug-in (www.plumed-code.org), and can be therefore readily used with multiple MD engines.
doi:10.1016/j.bpj.2015.05.024 pmid:26083917 pmcid:PMC4472218 fatcat:wjml25lz6vbevfcsn5jdm3s7xy

Automated Selection of Software Components Based on Cost/Reliability Tradeoff [chapter]

Vittorio Cortellessa, Fabrizio Marinelli, Pasqualina Potena
2006 Lecture Notes in Computer Science  
Estimation of the component testability The testability T estab ij of the j-th in-house instance available for the i-th component can be estimated before its implementation using model-based testing. An overview of model-based testing can be found in [2] . In the following we briefly propose a procedure to estimate the testability. We assume to have a set of UML diagrams that describe the dynamic behaviour of a component instance. If the diagrams are incomplete or inconsistent, then the
more » ... in [2] can be adopted to define a reasonably complete and consistent set of diagrams for model-testing. We suggest to apply model-based fault injection techniques to the consistent set of UML diagrams to estimate the component testability. A successful model-based fault injection technique has been introduced in [1], where authors inject faults in the architectural specification of a system to validate their analytical study on error propagation at the architectural level. For example, they devise the swapping of messages exchanged over the interactions of the UML Sequence Diagrams describing the component dynamics. The test cases to apply to the modified component model can be generated with the Use Interaction Test (UIT) method [2] , that automatically derives test cases by using information extracted from Sequence Diagrams. A simulation-based tool can then be used to observe the model behavior on the test cases. Mili et al. in [1] have adopted Rational Rose Real Time to validate their error propagation model. Derivation of the probability of failure on demand for in-house components In this section we formulate the probability of failure on demand for in-house components as a function of: (i) the probability p ij that the instance is faulty; (ii) the testability T estab ij , (iii) the number N suc ij of successful test cases performed. In other words we express the possibility of reducing the probability that the instance j of the component i fails by means of a certain amount of test cases represented by the variable N tot ij , which can be obtained from the following equation: N suc ij = (1 − T estab ij )N tot ij . Let A be the event "N suc ij failure-free test cases have been performed" and B be the event "the instance is faultfree". If ρ ij is the probability that the in-house developed instance is fault-free given that N suc ij test cases have been successfully performed, from the Bayes's theorem we get: ρ ij = P (B|A) = P (A|B)P (B) P (A|B)P (B) + P (A|B)P (B) The following equalities come straightforwardly: Therefore we have: Now we can define the probability of failure on demand θ ij of the in-house developed instance C ij , j ∈J i " under the assumption that the on-field users' operational profile is the same as that one adopted for testing [3] : and, by substituting ρ ij , we get equation 7, that is:
doi:10.1007/11966104_6 fatcat:isrbsvsajfgzxpjs37cmr6f7ie

Retropharyngeal lipoma causing sleep apnea syndrome

Stefano Di Girolamo, Luca Marinelli, Alessandra Galli, Fabrizio Ottaviani
1998 Journal of oral and maxillofacial surgery  
358, 1993 (letter) J Oral Maxlllofac Surg 56: 1003-l 004, 1998 Retropharyngeal Lipoma Causing Sleep Apnea Syndrome Stefano Di Girolamo, MD, * Luca Marine&, MD, f Alessandra Galli, MD,f and Fabrizio  ... 
doi:10.1016/s0278-2391(98)90668-1 pmid:9710200 fatcat:rfws6cz2knc27kobn5ogf3bgzq

Weighted force analysis method for derivation of multidimensional free energy landscapes from adaptively-biased replica simulations [article]

Fabrizio Marinelli, José D. Faraldo-Gómez
2021 bioRxiv   pre-print
AbstractA methodology is proposed for calculating multidimensional free-energy landscapes of molecular systems, based on post-hoc analysis of multiple molecular dynamics trajectories wherein adaptive biases are used to enhance the sampling of different collective variables. In this approach, which we refer to as Weighted Force Analysis Method (WFAM), sampling and biasing forces from all trajectories are suitably re-weighted and combined so as to obtain unbiased estimates of the mean force
more » ... collective-variable space; multidimensional free-energy surfaces and minimum-energy pathways are then derived from integration of the mean forces through kinetic Monte Carlo simulations. Numerical tests for trajectories of butyramide generated with standard and concurrent metadynamics, biased to sample one and two dihedral angles, respectively, demonstrate the correctness of the method and show that calculated mean forces and free energies converge rapidly. Analysis of bias-exchange metadynamics simulations of dialanine, trialanine and the SH2-SH3 domain-tandem of the Abl kinase, using up to six collective-variables, further demonstrate this approach greatly facilitates calculating accurate multidimensional free-energy landscapes from different trajectories and time-dependent biases, outperforming other post-hoc unbiasing methods.
doi:10.1101/2021.02.17.431654 fatcat:hbiagkdrwrcwdbbtaezbzos6ku

When "Chems" Meet Sex: A Rising Phenomenon Called "ChemSex"

Raffaele Giorgetti, Adriano Tagliabracci, Fabrizio Schifano, Simona Zaami, Enrico Marinelli, Francesco Paolo Busardò
2017 Current Neuropharmacology  
The term "chemsex" was coined to indicate the voluntary intake of psychoactive and non psychoactive drugs in the context of recreational settings to facilitate and/or to enhance sexual intercourses mostly among men who have sex with other men (MSM). Objective: The authors aimed to review the mechanisms of action, the toxicity and the pattern of use and abuse of substances involved in "chemsex" practice together with the sociocultural background underlying it and the health-related consequences
more » ... hat they may have. Results: Gamma-hydroxybutyrate, gamma-butyrolactone,1,4-butanediol, mephedrone, methamphetamine, sildenafil, tadalafil, vardenafil and alkyl nitrites have been described in their role of "chemsex drugs" including pharmacological action and in their implication to impair capacities to chose sexual partners and consensual sex. Moreover, it has been demonstrated that sexual activity over protracted length of time under the influence of chemsex drugs can result in rectal trauma or penile abrasions and a significant increase of the risk of transmission of sexual transmitted diseases, especially in case of condomless intercourses, which are frequent in this context, representing therefore a serious health threat. Conclusion: One of the major problems to establish health policy priority interventions for chemsex is the lack of available epidemiological data on the issue. Finally, social actions should be taken in order to break down the barriers that currently exist among chemsex drug users in accessing services, including the shame and stigma often associated with drug use. In conclusion, more specific resources to face high risks of infections and HIV transmission are required in bisexual and homosexual individuals having SUID: sex under the influence of drugs.
doi:10.2174/1570159x15666161117151148 pmid:27855594 pmcid:PMC5771052 fatcat:jwyrb2adpfcghaniww6436asca

Molecular Basis for Sodium Versus Calcium Binding in the Sodium-Calcium Exchanger

Fabrizio Marinelli, José D. Faraldo-Gómez
2014 Biophysical Journal  
Marinelli, José D.  ...  by NIH grants to DDT (R01 GM27906, P30 AR0507220), to SJG (AHA 13PRE13230005), and to SLR (R01 HL106189). 2164-Plat Molecular Basis for Sodium Versus Calcium Binding in the Sodium-Calcium Exchanger Fabrizio  ... 
doi:10.1016/j.bpj.2013.11.2410 fatcat:ovjdkvwembd4vom62pgvnv6adu

Minimally-Biased Metadynamics Method to Sample Conformational Ensembles Compatible with Experimental Measurements

Fabrizio Marinelli, José D. Faraldo-Gómez
2015 Biophysical Journal  
doi:10.1016/j.bpj.2014.11.873 fatcat:bbyp5an53vg67cqae3qsdlu4hq

Heterogeneous A40926 Self-Resistance Profile in Nonomuraea gerenzanensis Population Informs Strain Improvement

Elisa Binda, Francesca Berini, Flavia Marinelli, Adriana Bava, Fabrizio Beltrametti
2021 Fermentation  
Nonomuraea gerenzanensis ATCC 39727 produces the glycopeptide antibiotic A40926, which is the natural precursor of the semi-synthetic, last-resort drug dalbavancin. To reduce the cost of dalbavancin production, it is mandatory to improve the productivity of the producing strain. Here, we report that the exposure of N. gerenzanensis wild-type population to sub-inhibitory concentrations of A40926 led to the isolation of differently resistant phenotypes to which a diverse A40926 productivity was
more » ... sociated. The most resistant population (G, grand colonies) represented at least the 20% of the colonies growing on 2 µg/mL of A40926. It showed a stable phenotype after sub-culturing and a homogeneous profile of self-resistance to A40926 in population analysis profile (PAP) experiments. The less resistant population (P, petit) was represented by slow-growing colonies to which a lower A40926 productivity was associated. At bioreactor scale, the G variant produced twice more than the wild-type (ca. 400 mg/L A40926 versus less than 200 mg/L, respectively), paving the way for a rational strain improvement based on the selection of increasingly self-resistant colonies.
doi:10.3390/fermentation7030140 fatcat:u5gied7bmrertig6z4l5ec5qjq

METAGUI. A VMD interface for analyzing metadynamics and molecular dynamics simulations

Xevi Biarnés, Fabio Pietrucci, Fabrizio Marinelli, Alessandro Laio
2012 Computer Physics Communications  
We present a new computational tool, METAGUI, which extends the VMD program with a graphical user interface that allows constructing a thermodynamic and kinetic model of a given process simulated by large-scale molecular dynamics. The tool is specially designed for analyzing metadynamics based simulations. The huge amount of diverse structures generated during such a simulation is partitioned into a set of microstates (i.e. structures with similar values of the collective variables). Their
more » ... ive free energies are then computed by a weighted-histogram procedure and the most relevant free energy wells are identified by diagonalization of the rate matrix followed by a commitor analysis. All this procedure leads to a convenient representation of the metastable states and long-time kinetics of the system which can be compared with experimental data. The tool allows to seamlessly switch between a collective variables space representation of microstates and their atomic structure representation, which greatly facilitates the set-up and analysis of molecular dynamics simulations. METAGUI is based on the output format of the PLUMED plugin, making it compatible with a number of different molecular dynamics packages like AMBER, NAMD, GROMACS and several others. The METAGUI source files can be downloaded from the PLUMED web site (http://www.plumed-code.org). Program summary Program title: METAGUI Catalogue identifier: AEKH_v1_0 Program summary URL:
doi:10.1016/j.cpc.2011.08.020 fatcat:4ly4aabtdzhpbnmlfherszitu4

Cutting stock with no three parts per pattern: Work-in-process and pattern minimization

Alessandro Aloisio, Claudio Arbib, Fabrizio Marinelli
2011 Discrete Optimization  
The Pattern Minimization Problem (PMP) consists in finding, among the optimal solutions of a cutting stock problem, one that minimizes the number of distinct cutting patterns activated. The Work-in-process Minimization Problem (WMP) calls for scheduling the patterns so as to maintain as few open stacks as possible. This paper addresses a particular class of problems, where no more than two parts can be cut from any stock item, hence the feasible cutting patterns form the arc set of an
more » ... graph G. The paper extends the case G = K n introduced in 1999 by McDiarmid. We show that some properties holding for G = K n are no longer valid for the general case; however, for special cases of practical relevance, properly including G = K n , quasi-exact solutions for the PMP and the WMP can be found: the latter in polynomial time, the former via a set-packing formulation providing very good lower bounds.
doi:10.1016/j.disopt.2010.10.002 fatcat:zz62fvsn6zdntp2vemh4ornheu
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