Bayesian selection for coarse-grained models of liquid water

The necessity for accurate and computationally efficient representations of water in atomistic simulations that can span biologically relevant timescales has born the necessity of coarse-grained (CG) modeling. Despite numerous advances, CG water models rely mostly on a-priori specified assumptions. How these assumptions affect the model accuracy, efficiency, and in particular transferability, has not been systematically investigated. Here we propose a data driven, comparison and selection for CG water models through a Hierarchical Bayesian framework. We examine CG water models that differ in their level of coarse-graining, structure, and number of interaction sites. We find that the importance of electrostatic interactions for the physical system under consideration is a dominant criterion for the model selection. Multi-site models are favored, unless the effects of water in electrostatic screening are not relevant, in which case the single site model is preferred due to its computational savings. The charge distribution is found to play an important role in the multi-site model's accuracy while the flexibility of the bonds/angles may only slightly improve the models. Furthermore, we find significant variations in the computational cost of these models. We present a data informed rationale for the selection of CG water models and provide guidance for future water model designs

PLASTICITY OF HUMAN TENDON’S MECHANICAL PROPERTIES: EFFECTS ON SPORT PERFORMANCE

INTRODUCTION: In the literature it is often mentioned, that the tendon is very relevant for the work producing capability of the muscle fibers and for the motion and the performance of the human body. During a given movement, strain energy can be stored in the tendon and this way the whole energy delivery of the muscle can be enhanced. Further, the higher elongation capability of the tendon with respect to the muscle fiber, allows a bigger change in length of the muscle-tendon unit. Therefore, the muscle fibers may work on a lower shortening velocity and as a consequence of the force-velocity relationship their force producing potential will be higher. Generally, the main functions of the tendon during locomotion are: (a) to transfer muscle forces to the skeleton (b) to store mechanical energy coming from the human body or/and from muscular work as strain energy and (c) to create favorable conditions for the muscle fibers to produce force as a result of the force-length-velocity relationship. A higher force potential of the muscle fibers due to the force-length-velocity relationship during submaximal contractions would decrease the volume of active muscle at a given force or a given rate of force generation and consequently would decrease the cost of force production. In the same manner during maximal muscle contractions (maximal activation level) the higher force potential of the muscle fibers will allow the muscles to exert higher forces. The reports about the influence of the non rigidity of the tendon on the effectivity of muscle force production reveal the expectation that sport performance during submaximal as well as maximal running intensities may be affected by the mechanical and morphological properties of the tendon. In a series of experiments we examined the mechanical properties of the lower extremities muscle-tendon units (MTU) from athletes displaying different running economy and sprint performance. The most economical runners showed a higher contractile strength and a higher tendon stiffness in the triceps surae MTU and a higher compliance of the quadriceps tendon and aponeurosis at low level tendon forces (Arampatzis et al., 2006). The faster sprinters exhibited a higher elongation of the vastus lateralis (VL) tendon and aponeurosis at a given tendon force and a higher maximal elongation of the VL tendon and aponeurosis during the MVC (Stafilidis and Arampatzis, 2007). Furthermore, the maximal elongation of the VL tendon and aponeurosis showed a significant correlation with the 100 m sprint times (r = -0.567, P = 0.003). It has been supposed that, the more compliant quadriceps tendon and aponeurosis will increase the energy storage and return as well as the force potential of the muscle due to the force-velocity relationship. These studies provide evidence that the mechanical properties of the tendons at the lower extremity at least partially explain the performance of the human musculoskeletal system during running activities. However, until now no study exist in reference to the potential for improving running performance by manipulating the tendon mechanical properties. Mechanical load induced as cyclic strain on connective soft tissues such as tendons is an important regulator of fibroblast metabolic activity as well as for the maintenance of tendon matrix (Chiquet et al., 2003). An increased loading typically stimulates cells for remodelling and, therefore, for increasing the mechanical properties of the tissue (Arnoczky et al., 2002). Whereas, a decreased loading leads to tissue destruction and weak mechanical properties of the tissue (Arnoczky et al., 2004). These reports demonstrate the highly plastic nature of tendons within the muscle-tendon unit of mammals and give evidence that tendon strain is an important mechanical factor regulating tendon properties. Generally, from a mechanobiological point of view strain magnitude, strain frequency, strain rate and strain duration of cells influence the cellular biochemical responses and the mechanical properties of collagen fascicles. Although it is known that mechanical loading induced as cyclic strain affects the mechanical properties of human tendons in vivo, the effect of a controlled modulation in cyclic strain magnitude, frequency, rate or duration applied to the tendon on the plasticity of human tendons in vivo is not well established. Understanding the details of tendon plasticity in response to mechanical loading applied to the tendon in vivo may help to improve tendon adaptation, reduce tendon injury risks and increases the performance potential of the human system. This paper aimed (a) to present the effects of a controlled modulation of strain magnitude and strain frequency applied to the Achilles tendon on the plasticity of tendon mechanical and morphological properties and (b) to investigate whether an exercise induced increase in tendon-aponeurosis stiffness and contractile strength at the triceps surae muscle-tendon unit affect running economy

Goal-oriented sensitivity analysis for lattice kinetic Monte Carlo simulations

In this paper we propose a new class of coupling methods for the sensitivity analysis of high dimensional stochastic systems and in particular for lattice Kinetic Monte Carlo. Sensitivity analysis for stochastic systems is typically based on approximating continuous derivatives with respect to model parameters by the mean value of samples from a finite difference scheme. Instead of using independent samples the proposed algorithm reduces the variance of the estimator by developing a strongly correlated-"coupled"- stochastic process for both the perturbed and unperturbed stochastic processes, defined in a common state space. The novelty of our construction is that the new coupled process depends on the targeted observables, e.g. coverage, Hamiltonian, spatial correlations, surface roughness, etc., hence we refer to the proposed method as em goal-oriented sensitivity analysis. In particular, the rates of the coupled Continuous Time Markov Chain are obtained as solutions to a goal-oriented optimization problem, depending on the observable of interest, by considering the minimization functional of the corresponding variance. We show that this functional can be used as a diagnostic tool for the design and evaluation of different classes of couplings. Furthermore the resulting KMC sensitivity algorithm has an easy implementation that is based on the Bortz-Kalos-Lebowitz algorithm's philosophy, where here events are divided in classes depending on level sets of the observable of interest. Finally, we demonstrate in several examples including adsorption, desorption and diffusion Kinetic Monte Carlo that for the same confidence interval and observable, the proposed goal-oriented algorithm can be two orders of magnitude faster than existing coupling algorithms for spatial KMC such as the Common Random Number approach

Hierarchical fractional-step approximations and parallel kinetic Monte Carlo algorithms

We present a mathematical framework for constructing and analyzing parallel algorithms for lattice Kinetic Monte Carlo (KMC) simulations. The resulting algorithms have the capacity to simulate a wide range of spatio-temporal scales in spatially distributed, non-equilibrium physiochemical processes with complex chemistry and transport micro-mechanisms. The algorithms can be tailored to specific hierarchical parallel architectures such as multi-core processors or clusters of Graphical Processing Units (GPUs). The proposed parallel algorithms are controlled-error approximations of kinetic Monte Carlo algorithms, departing from the predominant paradigm of creating parallel KMC algorithms with exactly the same master equation as the serial one. Our methodology relies on a spatial decomposition of the Markov operator underlying the KMC algorithm into a hierarchy of operators corresponding to the processors' structure in the parallel architecture. Based on this operator decomposition, we formulate Fractional Step Approximation schemes by employing the Trotter Theorem and its random variants; these schemes, (a) determine the communication schedule} between processors, and (b) are run independently on each processor through a serial KMC simulation, called a kernel, on each fractional step time-window. Furthermore, the proposed mathematical framework allows us to rigorously justify the numerical and statistical consistency of the proposed algorithms, showing the convergence of our approximating schemes to the original serial KMC. The approach also provides a systematic evaluation of different processor communicating schedules.Comment: 34 pages, 9 figure

Antler artifacts from the Neolithic lakeside settlement Anarghiri IXb, Western Macedonia, Greece

The thesis addresses antler working and antler artifacts from the Neolithic lakeside settlement of Anarghiri IXb which is located in the Four Lakes region in Western Macedonia, Greece. This research contributes to our current understanding of the antler working in the Neolithic lakeside settlements of Western Macedonia in Greece by examining the biggest so far unearthed assemblage in Greece. The goal of this research is to establish a typology of the collected worked antler assemblage, to reveal the preferences of raw material, to reconstruct the manufacturing stages of the artifacts and to highlight the differences of antler exploitation in the habitation phases of the settlement. The study that was conducted from 2016 to 2018 brought to light interesting aspects concerning the use of antler in various everyday activities. Red deer antler prevails in the assemblage diachronically and antler was used mainly for the manufacture of tools that were used in woodworking activities or soil digging. Moreover, antler was used for the manufacture of hunting and fishing equipment and for the shaping of personal ornaments such as pendants and rings. A big part of the assemblage consists of blanks and waste material which shows that part of the manufacture was held inside the settlement. The attribution of the artifacts to the habitation phases of the settlements provided interesting information about the continuity of various tool forms and more importantly it provided a worked antler typology from the end of the 6th mil BC to the end of the 5th mil BC

Optimal sensing for fish school identification

Fish schooling implies an awareness of the swimmers for their companions. In flow mediated environments, in addition to visual cues, pressure and shear sensors on the fish body are critical for providing quantitative information that assists the quantification of proximity to other swimmers. Here we examine the distribution of sensors on the surface of an artificial swimmer so that it can optimally identify a leading group of swimmers. We employ Bayesian experimental design coupled with two-dimensional Navier Stokes equations for multiple self-propelled swimmers. The follower tracks the school using information from its own surface pressure and shear stress. We demonstrate that the optimal sensor distribution of the follower is qualitatively similar to the distribution of neuromasts on fish. Our results show that it is possible to identify accurately the center of mass and even the number of the leading swimmers using surface only information