Search

This article is devoted to the analysis of inverse source problems for Stokes systems in unbounded domains where the corresponding velocity flow is observed on a surface. Our main objective is to study the unique determination of general class of time-dependent and vector-valued source terms with potentially unknown divergence. Taking into account the challenges inherent in this class of inverse source problems, we aim to identify the most precise conditions that ensure their resolution. Motivated by various fluid motion problems, we explore several class of boundary measurements. Our proofs are based on different arguments, including unique continuation properties for Stokes systems, approximate controllability, complex analysis, and the application of explicit harmonic functions and explicit solutions for Stokes systems. This analysis is complemented by a reconstruction algorithm and examples of numerical computations.

It has become common to perform kinetic analysis using approximate Koopman operators that transforms high-dimensional time series of observables into ranked dynamical modes. Key to a practical success of the approach is the identification of a set of observables which form a good basis in which to expand the slow relaxation modes. Good observables are, however, difficult to identify {\em a priori} and sub-optimal choices can lead to significant underestimations of characteristic timescales. Leveraging the representation of slow dynamics in terms of Hidden Markov Model (HMM), we propose a simple and computationally efficient clustering procedure to infer surrogate observables that form a good basis for slow modes. We apply the approach to an analytically solvable model system, as well as on three protein systems of different complexities. We consistently demonstrate that the inferred indicator functions can significantly improve the estimation of the leading eigenvalues of the Koopman operators and correctly identify key states and transition timescales of stochastic systems, even when good observables are not known {\em a priori}., Comment: 28 pages, 6 figures

In this paper we study the hydrostatic limit of the Navier-Stokes-alpha model in a very thin striped domain. We derive some Prandtl-type limit equations for this model and we prove the global well-posedness of the limit system for small initial conditions in an appropriate analytic function space., Comment: Premi{\`e}re version, 33 pages

We demonstrate a machine learning approach designed to extract hidden chemistry/physics to facilitate new materials discovery. In particular, we propose a novel method for learning latent knowledge from material structure data in which machine learning models are developed to present the possibility that an atom can be paired with a chemical environment in an observed materials. For this purpose, we trained deep neural networks acquiring information from the atom of interest and its environment to estimate the possibility. The models were then used to establish recommendation systems, which can suggest a list of atoms for an environment within a structure. The center atom of that environment was then replaced with the various recommended atoms to generate new structures. Based on these recommendations, we also propose a method of dissimilarity measurement between the atoms and, through hierarchical cluster analysis and visualization using the multidimensional scaling algorithm, illustrate that this dissimilarity can reflect the chemistry of the elements. Finally, our models were applied to the discovery of new structures in the well-known magnetic material Nd$_2$Fe$_{14}$B. Our models propose 108 new structures, 71 of which are confirmed to converge to local-minimum-energy structures with formation energy less than 0.1 eV by first-principles calculations., Comment: 7pages, 6 figures

We prove the global wellposedness of the 2D non-rotating primitive equations with no-slip boundary conditions in a thin strip of width $\eps$ for small data which are analytic in the tangential direction. We also prove that the hydrostatic limit (when $\eps \to 0$) is a couple of a Prandtl-like system for the velocity with a transport-diffusion equation for the temperature., Comment: v2, 36 pages

This paper deals with the controllability of the second grade fluids, a class of non-Newtonian of differentiel type, on a two-dimensional torus. Using the method of Agrachev-Sarychev [1], [2] and of Sirikyan [26], we prove that the system of second grade fluids is approximately controllable by a finite-dimensional control force.

According to the nonequilibrium work relations, path-ensembles generated by irreversible processes in which a system is driven out of equilibrium according to a predetermined protocol may be used to compute equilibrium free energy differences and expectation values. Estimation has previously been improved by considering data collected from the reverse process, which starts in equilibrium in the final thermodynamic state of the forward process and is driven according to the time-reversed protocol. Here, we develop a theoretically rigorous statistical estimator for nonequilibrium path-ensemble averages specialized for symmetric protocols, in which forward and reverse processes are identical. The estimator is tested with a number of model systems: a symmetric 1D potential, an asymmetric 1D potential, the unfolding of deca-alanine, separating a host-guest system, and translocating a potassium ion through a gramicidin A ion channel. When reconstructing free energies using data from symmetric protocols, the new estimator outperforms existing rigorous unidirectional and bidirectional estimators, converging more quickly and resulting in smaller error. However, in most cases, using the bidirectional estimator with data from a forward and reverse pair of asymmetric protocols outperforms the corresponding symmetric protocol and estimator with the same amount of simulation time. Hence, the new estimator is only recommended when the bidirectional estimator is not feasible or is expected to perform poorly. The symmetric estimator has similar performance to a unidirectional protocol of half the length and twice the number of trajectories., Comment: 27 pages, 6 figures

The present work is devoted to the analysis of density-dependent, incompressible fluids in a 3D torus, when the Froude number $\varepsilon$ goes to zero. We consider the very general case where the initial data do not have a zero horizontal average, where we only have smoothing effect on the velocity but not on the density and where we can have resonant phenomena on the domain. We explicitly determine the limit system when $\varepsilon \to 0$ and prove its global wellposedness. Finally, we prove that for large initial data, the density-dependent, incompressible fluid system is globally wellposed, provided that $\varepsilon$ is small enough., Comment: submitted

We propose a novel type system for verifying that programs correctly implement constant-resource behavior. Our type system extends recent work on automatic amortized resource analysis (AARA), a set of techniques that automatically derive provable upper bounds on the resource consumption of programs. We devise new techniques that build on the potential method to achieve compositionality, precision, and automation. A strict global requirement that a program always maintains constant resource usage is too restrictive for most practical applications. It is sufficient to require that the program's resource behavior remain constant with respect to an attacker who is only allowed to observe part of the program's state and behavior. To account for this, our type system incorporates information flow tracking into its resource analysis. This allows our system to certify programs that need to violate the constant-time requirement in certain cases, as long as doing so does not leak confidential information to attackers. We formalize this guarantee by defining a new notion of resource-aware noninterference, and prove that our system enforces it. Finally, we show how our type inference algorithm can be used to synthesize a constant-time implementation from one that cannot be verified as secure, effectively repairing insecure programs automatically. We also show how a second novel AARA system that computes lower bounds on resource usage can be used to derive quantitative bounds on the amount of information that a program leaks through its resource use. We implemented each of these systems in Resource Aware ML, and show that it can be applied to verify constant-time behavior in a number of applications including encryption and decryption routines, database queries, and other resource-aware functionality., Comment: 30, IEEE S&P 2017

Transaction-level modeling with SystemC has been very successful in describing the behavior of embedded systems by providing high-level executable models, in which many of them have inherent probabilistic behaviors, e.g., random data and unreliable components. It thus is crucial to have both quantitative and qualitative analysis of the probabilities of system properties. Such analysis can be conducted by constructing a formal model of the system under verification and using Probabilistic Model Checking (PMC). However, this method is infeasible for large systems, due to the state space explosion. In this article, we demonstrate the successful use of Statistical Model Checking (SMC) to carry out such analysis directly from large SystemC models and allow designers to express a wide range of useful properties. The first contribution of this work is a framework to verify properties expressed in Bounded Linear Temporal Logic (BLTL) for SystemC models with both timed and probabilistic characteristics. Second, the framework allows users to expose a rich set of user-code primitives as atomic propositions in BLTL. Moreover, users can define their own fine-grained time resolution rather than the boundary of clock cycles in the SystemC simulation. The third contribution is an implementation of a statistical model checker. It contains an automatic monitor generation for producing execution traces of the model-under-verification (MUV), the mechanism for automatically instrumenting the MUV, and the interaction with statistical model checking algorithms., Comment: Journal of Software: Evolution and Process. Wiley, 2017. arXiv admin note: substantial text overlap with arXiv:1507.08187

This paper presents a new static analysis for deriving upper bounds on the expected resource consumption of probabilistic programs. The analysis is fully automatic and derives symbolic bounds that are multivariate polynomials of the inputs. The new technique combines manual state-of-the-art reasoning techniques for probabilistic programs with an effective method for automatic resource-bound analysis of deterministic programs. It can be seen as both, an extension of automatic amortized resource analysis (AARA) to probabilistic programs and an automation of manual reasoning for probabilistic programs that is based on weakest preconditions. As a result, bound inference can be reduced to off-the-shelf LP solving in many cases and automatically-derived bounds can be interactively extended with standard program logics if the automation fails. Building on existing work, the soundness of the analysis is proved with respect to an operational semantics that is based on Markov decision processes. The effectiveness of the technique is demonstrated with a prototype implementation that is used to automatically analyze 39 challenging probabilistic programs and randomized algorithms. Experimental results indicate that the derived constant factors in the bounds are very precise and even optimal for many programs.

We consider a system describing the motion of an isentropic, inviscid, weakly com-pressible, fast rotating fluid in the whole space R^3 , with initial data belonging to H^s(R^3) , s \textgreater{} 5/2. We prove that the system admits a unique local strong solution in L^$\infty$([0, T ]; H^s(R^3)) , where T is independent of the Rossby and Mach numbers. Moreover, using Strichartz-type estimates, we prove that the solution is almost global, i.e. its lifespan is of the order of $\epsilon$^(--$\alpha$) , $\alpha$ \textgreater{} 0, without any smallness assumption on the initial data (the initial data can even go to infinity in some sense), provided that the rotation is fast enough., Comment: Revised version

It is well known that, for fast rotating fluids with the axis of rotation being perpendicular to the boundary, the boundary layer is of Ekman-type, described by a linear ODE system. In this paper we consider fast rotating fluids, with the axis of rotation being parallel to the boundary. We show that the corresponding boundary layer is describe by a nonlinear, degenerated PDE system which is similar to the 2-D Prandtl system. Finally, we prove the well-posedness of the governing system of the boundary layer in the space of analytic functions with respect to tangential variable.

We study an anisotropic system arising in magnetohydrodynamics (MHD) in the whole space R^3 , in the case where there are no diffusivity in the vertical direction and only a small diffusivity in the horizontal direction (of size $\epsilon$$\alpha$ with 0 \textless{} $\alpha$ $\le$ $\alpha$0, for some $\alpha$0 \textgreater{} 0). We prove the local existence and uniqueness of a strong solution and then, using Strichartz-type estimates, we prove that this solution globally exists in time for large initial data, when the rotation is fast enough.

Stochastic Petri nets are commonly used for modeling distributed systems in order to study their performance and dependability. This paper proposes a realization of stochastic Petri nets in SystemC for modeling large embedded control systems. Then statistical model checking is used to analyze the dependability of the constructed model. Our verification framework allows users to express a wide range of useful properties to be verified which is illustrated through a case study.

Many embedded and real-time systems have a inherent probabilistic behaviour (sensors data, unreliable hardware,...). In that context, it is crucial to evaluate system properties such as "the probability that a particular hardware fails". Such properties can be evaluated by using probabilistic model checking. However, this technique fails on models representing realistic embedded and real-time systems because of the state space explosion. To overcome this problem, we propose a verification framework based on Statistical Model Checking. Our framework is able to evaluate probabilistic and temporal properties on large systems modelled in SystemC, a standard system-level modelling language. It is fully implemented as an extension of the Plasma-lab statistical model checker. We illustrate our approach on a multi-lift system case study.

We combine the formalisms of diagonal entropy and Jarzynski Equality to study the thermodynamic properties of closed quantum systems. Applying this approach to a quantum harmonic oscillator, the diagonal entropy offers a notion of temperature for closed systems away from equilibrium, and allows computing free-energy profiles. We also apply this approach to a hard-core boson lattice model, and discuss measures how to estimate temperature, entropy and measure work distribution functions. This technique offers a path to investigate the non-equilibrium quantum dynamics by means of performing work in a series of quenches., Comment: 6 pages and 4 figures

We present a generalization of Jarzynski's Equality, applicable to quantum systems, relating discretized mechanical work and free-energy changes. The theory is based on a step-wise pulling protocol. We find that work distribution functions can be constructed from fluctuations of a reaction coordinate along a reaction pathway in the step-wise pulling protocol. We also propose two sets of equations to determine the two possible optimal pathways that provide the most significant contributions to free-energy changes. We find that the transitions along these most optimal pathways, satisfying both sets of equations, follow the principle of detailed balance. We then test the theory by explicitly computing the free-energy changes for a one-dimensional quantum harmonic oscillator. This approach suggests a feasible way of measuring the fluctuations to experimentally test Jarzynski's Equality in many-body systems, such as Bose-Einstein condensates., Comment: 9 pages, 5 figures

Jarzynski's equality (JE) allows us to compute free energy differences from distributions of work. In molecular dynamics simulations, the traditional way of constructing work distributions is to perform as many pulling simulations as possible. But reliable work distributions are not always produced in a finite number of simulations. The computational cost of using JE is not less than other commonly used methods such as Thermodynamic Integration and Umbrella Sampling methods. Here we first show a different proof of JE based on the idea of step-wise pulling procedures that is efficient in computing free energies by using JE. The key point in our proof is that the processes of turning-on/off a harmonic potential to perform work are described by double Heaviside functions of time. We then show that the distributions of work performed by the potential can be easily generated from the distributions of a reaction coordinate along a pathway. Based on the proof, we propose sequential and parallel step-wise pulling protocols for generating work distributions that require suitable relaxation time at each pulling step. The criterion for reliable work distributions is that there must be sufficient mutual overlaps between the adjacent distributions of the reaction coordinate along the pathway. We arrive at an alternative formula (besides JE) to compute free energy differences from the averaged values of the reaction coordinate. The combination of JE and the alternative formula provides a viable way to determine the accuracy of computed free energy differences. For the stretching of a deca-alanine molecule, our approach requires 21 parallel simulations and relaxation time as small as 0.4 ns for each simulation to estimate free energy differences with an uncertainty of about 13%., Comment: 13 pages, 6 figures, 3 appendices

Jarzynski's equality [1] allows us to investigate free energy landscapes (FELs) by constructing distributions of work performed on a system from an initial ensemble of states to final states. This work is experimentally measured by extension-versus-force (EVF) curves. We proposed a new approach that enables us to reconstruct such FELs without necessity of measuring EVF curves. We proved that any free energy changes could be computed by measuring the fluctuations of a harmonic external potential in final states. The main assumption of our proof is that one should probably treat a potential's minimum {\lambda} (thought to be control parameter) and time in separate and independent manners. We recovered Jarzynski's equality from the introduction of a double Heaviside function. We then applied the approach in molecular dynamics (MD) simulations to compute the free energy barrier of breaking DNA base pairs (bps). The free energy barrier for breaking a CG bp in our simulations is identified as 1.7 +/- 0.2 kcal/mol that is in a very beautiful agreement with experimental values [2-4] of about 1.9 to 2.1 kcal/mol. Interestingly, the history of our computed free energies probably represents a favorable transition pathway., Comment: 5 main pages, 3 main figures, 10 pages for additional information. The DNA system is not appropriate for testing the theorem. A standardized system of a deca-alanine is chosen for further tests. The theorem is further developed and tested in another submitted paper